1) Present rules collect top for IDC
library(png)
library(grid)
eachIDCTopRules = list()
allIDCtoprules = c()
for (idx in 1:nrow(IDC)) {
############## first analysis
X = IDC[idx, 2:ncol(imgT2pLMSIRtest)]
y = IDC[idx, "lesion_label"]
rulesoutputIDC = mynewapplyLearnerxrules(topRulesIDC, X, y, minerr = 0.1, minfrq = 10/627, classes,
gbmModel)
topRulesIDC = rulesoutputIDC[[1]]
if (length(rulesoutputIDC) > 1) {
eachIDCTopRules[[idx]] = rulesoutputIDC[[2]]
allIDCtoprules = rbind(allIDCtoprules, rulesoutputIDC[[3]])
} else {
eachIDCTopRules[[idx]] = list()
allIDCtoprules = rbind(allIDCtoprules, 1:nrow(topRulesIDC) * 0)
}
}
[1] "test complies with # rules: 1 out of 50"
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# take the occurance of each explaining rule (columns) per case(row) + lesion identifies
df = data.frame(cbind(allIDCtoprules, as.character(IDC$allTestinfo.lesion_id), as.character(IDC$allTestinfo.lesion_label),
as.character(IDC$allTestinfo.lesion_diagnosis)), stringsAsFactors = FALSE)
colnames(df) <- c(as.character(1:nrow(topRulesIDC)), "lesion_id", "lesion_label", "lesion_diagnosis")
cols = 1:nrow(topRulesIDC)
df[, cols] = apply(df[, cols], 2, function(x) as.numeric(x))
cat(paste0("\n============== Top five explaining rules for InvasiveDuctal (IDC): n = ", nrow(IDC) +
2, "\n"))
============== Top five explaining rules for InvasiveDuctal (IDC): n = 136
topIDC = sort(colSums(df[, 1:nrow(topRulesIDC)]), decreasing = TRUE)
print(topIDC[1:5])
43 38 45 21 44
53 52 50 49 49
freqtopIDC = topIDC[1:5]
totalIDC = nrow(IDC) + 2
print(freqtopIDC/totalIDC)
43 38 45 21 44
0.3897059 0.3823529 0.3676471 0.3602941 0.3602941
rulesTopIDC = as.numeric(names(topIDC[1:5]))
preserulesTopIDC = mypresentRules(topRulesIDC[rulesTopIDC, ], colnames(X), fnames)
rownames(preserulesTopIDC) <- NULL
print(preserulesTopIDC)
len freq err
1 4 0.159 0.093
2 3 0.16 0.09
3 2 0.156 0.094
4 2 0.144 0.076
5 2 0.155 0.094
condition
1 irregularity medium to high & Variance ptime1 very high & Difference variance ptime4 very low to high & T2w Difference entropy low to very high
2 max relative signal enhancement(rim) medium to high & Variance ptime1 very high & Difference variance ptime2 very low to high
3 SER(in) medium to high & irregularity high
4 SER(in) medium to high & irregularity high
5 Variance ptime1 very high & dispersion s16 medium to high
pred prob sumtempProb Ruletype
1 C 0.7622081, 0.4384610, 0.4232979, 0.4466687 0.5176589 T1wmorphology & T1wtexture & T2w
2 C 0.8237662, 0.4610768, 0.7663881 0.6837437 T1wdynamic & T1wtexture
3 C 0.7579719, 0.4714506 0.6147112 T1wdynamic & T1wmorphology
4 C 0.5006988, 0.6626664 0.5816826 T1wdynamic & T1wmorphology
5 C 0.4291609, 0.7692691 0.599215 T1wtexture & dispersion
# display a case that meets them all
casesIDC = df[, c(rulesTopIDC, nrow(topRulesIDC) + 1, nrow(topRulesIDC) + 2, nrow(topRulesIDC) +
3)]
print("Sorted cases meeting top five explaining rules for InvasiveDuctal (IDC):")
[1] "Sorted cases meeting top five explaining rules for InvasiveDuctal (IDC):"
topcasesIDC = casesIDC[sort(rowSums(casesIDC[, 1:5]), index = TRUE, decreasing = TRUE)$ix, ]
print(topcasesIDC)
43 38 45 21 44 lesion_id lesion_label lesion_diagnosis
10 1 1 1 1 1 515 nonmassM InvasiveDuctal
11 1 1 1 1 1 538 massM InvasiveDuctal
19 1 1 1 1 1 235 massM InvasiveDuctal
21 1 1 1 1 1 299 massM InvasiveDuctal
44 1 1 1 1 1 168 massM InvasiveDuctal
49 1 1 1 1 1 320 massM InvasiveDuctal
51 1 1 1 1 1 397 massM InvasiveDuctal
52 1 1 1 1 1 430 massM InvasiveDuctal
58 1 1 1 1 1 199 massM InvasiveDuctal
59 1 1 1 1 1 200 massM InvasiveDuctal
63 1 1 1 1 1 544 massM InvasiveDuctal
75 1 1 1 1 1 341 massM InvasiveDuctal
77 1 1 1 1 1 417 massM InvasiveDuctal
80 1 1 1 1 1 154 massM InvasiveDuctal
83 1 1 1 1 1 169 massM InvasiveDuctal
92 1 1 1 1 1 560 massM InvasiveDuctal
93 1 1 1 1 1 561 massM InvasiveDuctal
94 1 1 1 1 1 567 massM InvasiveDuctal
103 1 1 1 1 1 241 massM InvasiveDuctal
104 1 1 1 1 1 280 massM InvasiveDuctal
109 1 1 1 1 1 554 massM InvasiveDuctal
119 1 1 1 1 1 160 massM InvasiveDuctal
124 1 1 1 1 1 392 nonmassM InvasiveDuctal
128 1 1 1 1 1 520 massM InvasiveDuctal
130 1 1 1 1 1 526 massM InvasiveDuctal
131 1 1 1 1 1 527 nonmassM InvasiveDuctal
133 1 1 1 1 1 529 massM InvasiveDuctal
5 1 1 1 1 0 217 massM InvasiveDuctal
24 1 0 1 1 1 398 nonmassM InvasiveDuctal
37 1 0 1 1 1 404 massM InvasiveDuctal
45 0 1 1 1 1 182 massM InvasiveDuctal
53 1 0 1 1 1 559 massM InvasiveDuctal
88 1 1 1 0 1 394 massM InvasiveDuctal
117 1 1 0 1 1 504 massM InvasiveDuctal
120 1 0 1 1 1 161 nonmassM InvasiveDuctal
125 1 1 1 1 0 393 massM InvasiveDuctal
3 1 1 0 0 1 153 massM InvasiveDuctal
9 1 1 0 0 1 514 massM InvasiveDuctal
12 1 1 0 0 1 539 massM InvasiveDuctal
15 0 1 1 1 0 139 massM InvasiveDuctal
18 1 1 0 0 1 209 nonmassM InvasiveDuctal
31 1 1 0 0 1 121 massM InvasiveDuctal
34 1 1 0 0 1 171 massM InvasiveDuctal
41 1 1 0 0 1 12 nonmassM InvasiveDuctal
42 1 1 0 0 1 149 massM InvasiveDuctal
60 1 1 0 0 1 210 massM InvasiveDuctal
105 1 1 0 0 1 281 nonmassM InvasiveDuctal
110 1 1 0 0 1 569 massM InvasiveDuctal
8 0 0 1 1 0 424 massM InvasiveDuctal
16 0 0 1 1 0 172 massM InvasiveDuctal
20 0 0 1 0 1 282 nonmassM InvasiveDuctal
29 1 1 0 0 0 513 massM InvasiveDuctal
30 0 0 1 1 0 570 nonmassM InvasiveDuctal
33 0 1 0 0 1 124 massM InvasiveDuctal
36 0 0 1 1 0 303 massM InvasiveDuctal
38 0 0 1 1 0 498 nonmassM InvasiveDuctal
43 1 1 0 0 0 150 massM InvasiveDuctal
47 0 0 1 1 0 252 massM InvasiveDuctal
70 0 0 1 1 0 144 massM InvasiveDuctal
71 0 0 1 1 0 177 nonmassM InvasiveDuctal
74 0 0 1 1 0 257 nonmassM InvasiveDuctal
81 1 1 0 0 0 162 massM InvasiveDuctal
84 0 0 1 1 0 251 massM InvasiveDuctal
102 1 1 0 0 0 240 massM InvasiveDuctal
113 1 1 0 0 0 8 nonmassM InvasiveDuctal
114 0 0 1 1 0 9 nonmassM InvasiveDuctal
118 1 0 0 0 1 546 massM InvasiveDuctal
129 0 0 1 1 0 523 massM InvasiveDuctal
4 0 1 0 0 0 179 massM InvasiveDuctal
17 0 0 1 0 0 188 massM InvasiveDuctal
23 0 1 0 0 0 384 massM InvasiveDuctal
48 0 0 0 1 0 276 massM InvasiveDuctal
72 1 0 0 0 0 190 massM InvasiveDuctal
96 0 0 0 0 1 628 massM InvasiveDuctal
1 0 0 0 0 0 40 massM InvasiveDuctal
2 0 0 0 0 0 41 nonmassM InvasiveDuctal
6 0 0 0 0 0 229 massM InvasiveDuctal
7 0 0 0 0 0 380 massM InvasiveDuctal
13 0 0 0 0 0 540 nonmassM InvasiveDuctal
14 0 0 0 0 0 89 nonmassM InvasiveDuctal
22 0 0 0 0 0 360 massM InvasiveDuctal
25 0 0 0 0 0 457 massM InvasiveDuctal
26 0 0 0 0 0 487 massM InvasiveDuctal
27 0 0 0 0 0 490 massM InvasiveDuctal
28 0 0 0 0 0 506 nonmassM InvasiveDuctal
32 0 0 0 0 0 122 nonmassM InvasiveDuctal
35 0 0 0 0 0 230 massM InvasiveDuctal
39 0 0 0 0 0 552 massM InvasiveDuctal
40 0 0 0 0 0 578 massM InvasiveDuctal
46 0 0 0 0 0 189 massM InvasiveDuctal
50 0 0 0 0 0 321 nonmassM InvasiveDuctal
54 0 0 0 0 0 621 massM InvasiveDuctal
55 0 0 0 0 0 81 massM InvasiveDuctal
56 0 0 0 0 0 95 massM InvasiveDuctal
57 0 0 0 0 0 108 nonmassM InvasiveDuctal
61 0 0 0 0 0 247 massM InvasiveDuctal
62 0 0 0 0 0 401 massM InvasiveDuctal
64 0 0 0 0 0 545 massM InvasiveDuctal
65 0 0 0 0 0 555 massM InvasiveDuctal
66 0 0 0 0 0 556 massM InvasiveDuctal
67 0 0 0 0 0 620 massM InvasiveDuctal
68 0 0 0 0 0 142 massM InvasiveDuctal
69 0 0 0 0 0 143 nonmassM InvasiveDuctal
73 0 0 0 0 0 215 massM InvasiveDuctal
76 0 0 0 0 0 403 massM InvasiveDuctal
78 0 0 0 0 0 494 nonmassM InvasiveDuctal
79 0 0 0 0 0 88 massM InvasiveDuctal
82 0 0 0 0 0 163 massM InvasiveDuctal
85 0 0 0 0 0 260 massM InvasiveDuctal
86 0 0 0 0 0 329 nonmassM InvasiveDuctal
87 0 0 0 0 0 350 massM InvasiveDuctal
89 0 0 0 0 0 541 massM InvasiveDuctal
90 0 0 0 0 0 542 massM InvasiveDuctal
91 0 0 0 0 0 543 massM InvasiveDuctal
95 0 0 0 0 0 580 massM InvasiveDuctal
97 0 0 0 0 0 67 massM InvasiveDuctal
98 0 0 0 0 0 68 massM InvasiveDuctal
99 0 0 0 0 0 111 massM InvasiveDuctal
100 0 0 0 0 0 126 massM InvasiveDuctal
101 0 0 0 0 0 136 massM InvasiveDuctal
106 0 0 0 0 0 444 massM InvasiveDuctal
107 0 0 0 0 0 447 massM InvasiveDuctal
108 0 0 0 0 0 553 massM InvasiveDuctal
111 0 0 0 0 0 589 massM InvasiveDuctal
112 0 0 0 0 0 626 massM InvasiveDuctal
115 0 0 0 0 0 106 massM InvasiveDuctal
116 0 0 0 0 0 495 massM InvasiveDuctal
121 0 0 0 0 0 238 massM InvasiveDuctal
122 0 0 0 0 0 265 massM InvasiveDuctal
123 0 0 0 0 0 337 nonmassM InvasiveDuctal
126 0 0 0 0 0 441 nonmassM InvasiveDuctal
127 0 0 0 0 0 512 massM InvasiveDuctal
132 0 0 0 0 0 528 massM InvasiveDuctal
134 0 0 0 0 0 530 nonmassM InvasiveDuctal
print("Fine explaining rules for InvasiveDuctal (IDC) with LMSIR:")
[1] "Fine explaining rules for InvasiveDuctal (IDC) with LMSIR:"
LMSIRfeatureflag = c()
idLMSIR = c()
for (i in 1:length(eachIDCTopRules)) {
if (length(eachIDCTopRules[[i]]) > 0) {
rules = mypresentRules(eachIDCTopRules[[i]], colnames(X), fnames)
LMSIRwtop5 = "LMSIR" %in% unlist(strsplit(unlist(strsplit(rules$condition, split = " & ")),
split = " "))
if (LMSIRwtop5) {
LMSIRfeatureflag = c(LMSIRfeatureflag, LMSIRwtop5)
print(i)
print(rules)
idLMSIR = c(idLMSIR, i)
} else {
LMSIRfeatureflag = c(LMSIRfeatureflag, FALSE)
}
} else {
LMSIRfeatureflag = c(LMSIRfeatureflag, FALSE)
}
}
[1] 46
len freq err
3868 3 0.031 0.0590000000000001
300 3 0.115 0.081
condition pred
3868 dispersion s15 low to very high & 3rd post-SE s4 high & predicted LMSIR very low C
300 SER(in) medium to high & uptake skewness low & irregularity medium to high C
prob sumtempProb Ruletype
3868 0.4853810, 0.6962119, 0.4631950 0.5482627 dispersion & single-time-Enh & T2w
300 0.5949279, 0.7518615, 0.4569649 0.6012514 T1wdynamic & T1wmorphology
[1] 56
len freq err
3868 3 0.031 0.0590000000000001
4999 3 0.059 0.0620000000000001
442 3 0.237 0.07
858 2 0.062 0.088
condition pred
3868 dispersion s15 low to very high & 3rd post-SE s4 high & predicted LMSIR very low C
4999 uptake average high & 1st post-SE s8 high & T2w Correlation low C
442 irregularity low & Variance ptime2 low to medium & Energy ptime4 very low to high NC
858 SER(in) medium to high & Max Radial gradient variance very low NC
prob sumtempProb Ruletype
3868 0.4853810, 0.6962119, 0.4631950 0.5482627 dispersion & single-time-Enh & T2w
4999 0.3727659, 0.5435277, 0.4635614 0.4599517 T1wdynamic & single-time-Enh & T2w
442 0.4378788, 0.2352466, 0.2721108 0.3150787 T1wmorphology & T1wtexture
858 0.4812519, 0.5830327 0.5321423 T1wdynamic & T1wmorphology
[1] 87
len freq err
68 3 0.111 0.049
3868 3 0.031 0.0590000000000001
4999 3 0.059 0.0620000000000001
300 3 0.115 0.081
condition pred
68 Initial Uptake slope(in) high & uptake skewness low & irregularity medium to high C
3868 dispersion s15 low to very high & 3rd post-SE s4 high & predicted LMSIR very low C
4999 uptake average high & 1st post-SE s8 high & T2w Correlation low C
300 SER(in) medium to high & uptake skewness low & irregularity medium to high C
prob sumtempProb Ruletype
68 0.4479334, 0.7561858, 0.6379134 0.6140108 T1wdynamic & T1wmorphology
3868 0.4853810, 0.6962119, 0.4631950 0.5482627 dispersion & single-time-Enh & T2w
4999 0.3727659, 0.5435277, 0.4635614 0.4599517 T1wdynamic & single-time-Enh & T2w
300 0.5949279, 0.7518615, 0.4569649 0.6012514 T1wdynamic & T1wmorphology
[1] 89
len freq err
10957 5 0.051 0
68 3 0.111 0.049
3868 3 0.031 0.0590000000000001
4999 3 0.059 0.0620000000000001
2791 3 0.117 0.078
2963 3 0.091 0.08
300 3 0.115 0.081
124 3 0.133 0.097
condition
10957 Time-to-peak(in) low & Variance of spatial Margin Gradient very low to high & circularity low & dispersion s12 very low to high & dispersion s17 low to medium
68 Initial Uptake slope(in) high & uptake skewness low & irregularity medium to high
3868 dispersion s15 low to very high & 3rd post-SE s4 high & predicted LMSIR very low
4999 uptake average high & 1st post-SE s8 high & T2w Correlation low
2791 Time-to-peak(in) low & circularity low & Max Radial gradient variance low to very high
2963 uptake average high & Energy ptime4 very low to high & last post-SE s2 high
300 SER(in) medium to high & uptake skewness low & irregularity medium to high
124 Time-to-peak(in) low & Rate of signal increase(rim) medium to high & irregularity medium to high
pred prob sumtempProb
10957 C 0.5682319, 0.6838746, 0.4879725, 0.4530955, 0.4300886 0.5246526
68 C 0.4479334, 0.7561858, 0.6379134 0.6140108
3868 C 0.4853810, 0.6962119, 0.4631950 0.5482627
4999 C 0.3727659, 0.5435277, 0.4635614 0.4599517
2791 C 0.6633012, 0.5110174, 0.6863620 0.6202269
2963 C 0.4627302, 0.4869596, 0.5895322 0.513074
300 C 0.5949279, 0.7518615, 0.4569649 0.6012514
124 C 0.7280304, 0.4252003, 0.5877582 0.5803296
Ruletype
10957 T1wdynamic & T1wmorphology & dispersion
68 T1wdynamic & T1wmorphology
3868 dispersion & single-time-Enh & T2w
4999 T1wdynamic & single-time-Enh & T2w
2791 T1wdynamic & T1wmorphology
2963 T1wdynamic & T1wtexture & single-time-Enh
300 T1wdynamic & T1wmorphology
124 T1wdynamic & T1wmorphology
[1] 95
len freq err
3868 3 0.031 0.0590000000000001
condition pred
3868 dispersion s15 low to very high & 3rd post-SE s4 high & predicted LMSIR very low C
prob sumtempProb Ruletype
3868 0.4853810, 0.6962119, 0.4631950 0.5482627 dispersion & single-time-Enh & T2w
[1] 111
len freq err
10957 5 0.051 0
3868 3 0.031 0.0590000000000001
2791 3 0.117 0.078
454 3 0.132 0.097
124 3 0.133 0.097
condition
10957 Time-to-peak(in) low & Variance of spatial Margin Gradient very low to high & circularity low & dispersion s12 very low to high & dispersion s17 low to medium
3868 dispersion s15 low to very high & 3rd post-SE s4 high & predicted LMSIR very low
2791 Time-to-peak(in) low & circularity low & Max Radial gradient variance low to very high
454 Time-to-peak(in) low & irregularity medium to high & 1st post-SE s12 medium to high
124 Time-to-peak(in) low & Rate of signal increase(rim) medium to high & irregularity medium to high
pred prob sumtempProb
10957 C 0.5682319, 0.6838746, 0.4879725, 0.4530955, 0.4300886 0.5246526
3868 C 0.4853810, 0.6962119, 0.4631950 0.5482627
2791 C 0.6633012, 0.5110174, 0.6863620 0.6202269
454 C 0.7569990, 0.5009352, 0.6581838 0.638706
124 C 0.7280304, 0.4252003, 0.5877582 0.5803296
Ruletype
10957 T1wdynamic & T1wmorphology & dispersion
3868 dispersion & single-time-Enh & T2w
2791 T1wdynamic & T1wmorphology
454 T1wdynamic & T1wmorphology & single-time-Enh
124 T1wdynamic & T1wmorphology
[1] 113
len freq err
420 3 0.148 0.049
3868 3 0.031 0.0590000000000001
2963 3 0.091 0.08
3524 2 0.043 0.087
182 2 0.123 0.088
62 3 0.16 0.09
10681 2 0.08 0.091
7286 4 0.159 0.093
2589 2 0.095 0.096
condition
420 Variance ptime1 very high & dispersion s16 low to very high & 3rd post-SE s6 medium to high
3868 dispersion s15 low to very high & 3rd post-SE s4 high & predicted LMSIR very low
2963 uptake average high & Energy ptime4 very low to high & last post-SE s2 high
3524 change in Variance of spatial Margin Gradient low & dispersion s17 very high
182 Variance ptime1 very high & dispersion s9 medium to high
62 max relative signal enhancement(rim) medium to high & Variance ptime1 very high & Difference variance ptime2 very low to high
10681 Difference variance ptime1 very high & Difference variance ptime2 very low to high
7286 irregularity medium to high & Variance ptime1 very high & Difference variance ptime4 very low to high & T2w Difference entropy low to very high
2589 Variance ptime2 very high & Difference variance ptime2 very low to high
pred prob sumtempProb
420 C 0.4705374, 0.8140437, 0.7544592 0.6796801
3868 C 0.4853810, 0.6962119, 0.4631950 0.5482627
2963 C 0.4627302, 0.4869596, 0.5895322 0.513074
3524 C 0.3885357, 0.5447962 0.466666
182 C 0.4279656, 0.7763369 0.6021512
62 C 0.8237662, 0.4610768, 0.7663881 0.6837437
10681 C 0.4832205, 0.4638078 0.4735142
7286 C 0.7622081, 0.4384610, 0.4232979, 0.4466687 0.5176589
2589 C 0.4973411, 0.4768212 0.4870812
Ruletype
420 T1wtexture & dispersion & single-time-Enh
3868 dispersion & single-time-Enh & T2w
2963 T1wdynamic & T1wtexture & single-time-Enh
3524 T1wmorphology & dispersion
182 T1wtexture & dispersion
62 T1wdynamic & T1wtexture
10681 T1wtexture
7286 T1wmorphology & T1wtexture & T2w
2589 T1wtexture
[1] 114
len freq err
1193 3 0.03 0
68 3 0.111 0.049
3868 3 0.031 0.0590000000000001
310 2 0.144 0.076
300 3 0.115 0.081
1063 3 0.067 0.081
3524 2 0.043 0.087
588 2 0.121 0.09
615 2 0.14 0.091
184 2 0.156 0.094
condition
1193 Time-to-peak(rim) medium to high & max Radial gradient low & T2w radial gradient variance low
68 Initial Uptake slope(in) high & uptake skewness low & irregularity medium to high
3868 dispersion s15 low to very high & 3rd post-SE s4 high & predicted LMSIR very low
310 SER(in) medium to high & irregularity high
300 SER(in) medium to high & uptake skewness low & irregularity medium to high
1063 irregularity high & Inverse difference moment ptime2 low to medium & 1st post-SE s8 high
3524 change in Variance of spatial Margin Gradient low & dispersion s17 very high
588 SER(in) high & irregularity high
615 irregularity high & 1st post-SE s15 medium to high
184 SER(in) medium to high & irregularity high
pred prob sumtempProb
1193 NC 0.4662758, 0.3631702, 0.5977509 0.4757323
68 C 0.4479334, 0.7561858, 0.6379134 0.6140108
3868 C 0.4853810, 0.6962119, 0.4631950 0.5482627
310 C 0.5006988, 0.6626664 0.5816826
300 C 0.5949279, 0.7518615, 0.4569649 0.6012514
1063 C 0.5128461, 0.6452170, 0.4944342 0.5508324
3524 C 0.3885357, 0.5447962 0.466666
588 C 0.4565346, 0.6397499 0.5481423
615 C 0.4819968, 0.7471799 0.6145883
184 C 0.7579719, 0.4714506 0.6147112
Ruletype
1193 T1wdynamic & T1wmorphology & T2w
68 T1wdynamic & T1wmorphology
3868 dispersion & single-time-Enh & T2w
310 T1wdynamic & T1wmorphology
300 T1wdynamic & T1wmorphology
1063 T1wmorphology & T1wtexture & single-time-Enh
3524 T1wmorphology & dispersion
588 T1wdynamic & T1wmorphology
615 T1wmorphology & single-time-Enh
184 T1wdynamic & T1wmorphology
[1] 126
len freq err
3499 4 0.031 0
4984 2 0.042 0.043
11396 3 0.063 0.0590000000000001
3868 3 0.031 0.0590000000000001
4999 3 0.059 0.0620000000000001
2963 3 0.091 0.08
7460 3 0.062 0.088
condition
3499 max uptake very high & Sum average ptime2 very low to high & last post-SE s8 low to very high & T2w Sum average low to very high
4984 max uptake very high & last post-SE s8 low to very high
11396 Washout rate(in) very high & Sum Entropy ptime1 very high & Entropy ptime1 very high
3868 dispersion s15 low to very high & 3rd post-SE s4 high & predicted LMSIR very low
4999 uptake average high & 1st post-SE s8 high & T2w Correlation low
2963 uptake average high & Energy ptime4 very low to high & last post-SE s2 high
7460 uptake average high & std 3D Sharpness of lesion margin high & last post-SE s18 medium to high
pred prob sumtempProb
3499 C 0.4648681, 0.4791564, 0.4145251, 0.4431299 0.4504199
4984 C 0.5415453, 0.4910949 0.5163201
11396 C 0.5191539, 0.4959777, 0.3986381 0.4712566
3868 C 0.4853810, 0.6962119, 0.4631950 0.5482627
4999 C 0.3727659, 0.5435277, 0.4635614 0.4599517
2963 C 0.4627302, 0.4869596, 0.5895322 0.513074
7460 C 0.2956963, 0.4250158, 0.5423104 0.4210075
Ruletype
3499 T1wdynamic & T1wtexture & single-time-Enh & T2w
4984 T1wdynamic & single-time-Enh
11396 T1wdynamic & T1wtexture
3868 dispersion & single-time-Enh & T2w
4999 T1wdynamic & single-time-Enh & T2w
2963 T1wdynamic & T1wtexture & single-time-Enh
7460 T1wdynamic & T1wmorphology & single-time-Enh
print(summary(LMSIRfeatureflag))
Mode FALSE TRUE NA's
logical 125 9 0
### display
lesion_id = 241
idx = c(1:nrow(IDC))[c(IDC$allTestinfo.lesion_id == lesion_id)]
infoidx = allTestinfo[allTestinfo$lesion_id == lesion_id, -c(20)]
print(infoidx)
lesion_id lesionfile cad_pt_no_txt anony_dob_datetime exam_img_dicom_txt
241 241 241_0817_5363917.vtk 0817 1970-07-04 00:00:00.000000 13171
exam_a_number_txt exam_dt_datetime exam_mri_cad_status_txt
241 5363917 2010-08-24 00:00:00.000000 Unknown
cad_latest_mutation_status_int exam_find_mri_mass_yn exam_find_mri_nonmass_yn
241 Other 1 0
exam_find_side_int proc_pt_procedure_id proc_proc_dt_datetime proc_proc_side_int
241 Right 2499 2010-09-08 00:00:00.000000 Right
proc_proc_source_int proc_proc_guid_int proc_proc_tp_int
241 Radiology MRI Vacuum Assisted Biopsy
proc_lesion_comments_txt
241 Investigation in Bangladesh of palpable abnormality 1\no'clock right breast with FNAB positive for malignancy. FNAB of\nprominent node negative for malignancy.
find_curve_int find_mri_dce_init_enh_int find_mri_dce_delay_enh_int BIRADS lesion_label
241 Ia Rapid Persistent 6 massM
lesion_diagnosis
241 InvasiveDuctal
cat(allTestinfo[allTestinfo$lesion_id == lesion_id, c(20)])
?<Report title=""Surgical Pathology Report""><Sessions>
Date: Sept 08, 2010
AP Report:
(NOTE)
SURGICAL PATHOLOGY REPORT
HFN: 2693587
Encounter #: 7323410R
Specimen #: S10-23904
CLINICAL INFORMATION
A) 14 G 4 cores. Probable FA. B) 14 G 4 cores. Known Ca by FNA and
receptors. Receptors please; ER/PR/Her2Neu.
SPECIMENS SUBMITTED
A: Right breast, core biopsy 9 o'clock
B: Right breast, core biopsy 1 o'clock
DIAGNOSIS
A. Breast, right, 9 o'clock, core biopsy:
- FIBROADENOMA
- PROLIFERATIVE FIBROCYSTIC CHANGES
- NO EVIDENCE OF MALIGNANCY
B. Breast, right, 1 o'clock, core biopsy:
- INVASIVE DUCTAL CARCINOMA, MICROPAPILLARY TYPE, INTERMEDIATE
DIFFERENTIATION
MACROSCOPIC DESCRIPTION
A. The specimen container is labeled with the patient name and 'right
breast biopsies site A 9H'. The accompanying requisition matches the
container's label.The specimen consists of 4 cores of tan hemorrhagic
and fatty tissue, each with a diameter of 0.1 cm, ranging from 0.8 to
1.5 cm in length. Submitted in toto in one block.
B. The specimen container is labeled with the patient name and 'right
breast biopsies site B 1H'. The accompanying requisition matches the
container's label.The specimen consists of 4 cores of tan hemorrhagic
and fatty tissue, each with a diameter of 0.1 cm, ranging from 0.6 to
1.5 cm in length. Submitted in toto in one block.
LS
Dictated 09/08/2010
Reda Saad, MD, FRCPC
Report Electronically Signed
2010/09/09 16:30
</Sessions></Report>
print(mypresentRules(eachIDCTopRules[[idx]], colnames(X), fnames))
len freq err
10957 5 0.051 0
322 2 0.113 0.049
420 3 0.148 0.049
68 3 0.111 0.049
9295 3 0.073 0.05
11396 3 0.063 0.0590000000000001
112 2 0.089 0.0610000000000001
4999 3 0.059 0.0620000000000001
40 2 0.132 0.069
670 3 0.079 0.07
310 2 0.144 0.076
12068 3 0.094 0.077
2791 3 0.117 0.078
2963 3 0.091 0.08
300 3 0.115 0.081
1063 3 0.067 0.081
455 2 0.128 0.085
7460 3 0.062 0.088
62 3 0.16 0.09
588 2 0.121 0.09
615 2 0.14 0.091
10681 2 0.08 0.091
85 2 0.138 0.092
7286 4 0.159 0.093
155 2 0.155 0.094
184 2 0.156 0.094
135 2 0.115 0.095
2589 2 0.095 0.096
511 2 0.13 0.097
454 3 0.132 0.097
124 3 0.133 0.097
condition
10957 Time-to-peak(in) low & Variance of spatial Margin Gradient very low to high & circularity low & dispersion s12 very low to high & dispersion s17 low to medium
322 irregularity high & Variance ptime1 high
420 Variance ptime1 very high & dispersion s16 low to very high & 3rd post-SE s6 medium to high
68 Initial Uptake slope(in) high & uptake skewness low & irregularity medium to high
9295 Time-to-peak(in) low & irregularity high & 1st post-SE s10 high
11396 Washout rate(in) very high & Sum Entropy ptime1 very high & Entropy ptime1 very high
112 irregularity very high & Sum variance ptime1 high
4999 uptake average high & 1st post-SE s8 high & T2w Correlation low
40 irregularity high & Variance ptime1 high
670 irregularity high & Variance ptime2 high & Sum Entropy ptime2 very high
310 SER(in) medium to high & irregularity high
12068 irregularity low to very high & Sum variance ptime1 very high & dispersion s18 medium to high
2791 Time-to-peak(in) low & circularity low & Max Radial gradient variance low to very high
2963 uptake average high & Energy ptime4 very low to high & last post-SE s2 high
300 SER(in) medium to high & uptake skewness low & irregularity medium to high
1063 irregularity high & Inverse difference moment ptime2 low to medium & 1st post-SE s8 high
455 SER(in) medium to high & irregularity high
7460 uptake average high & std 3D Sharpness of lesion margin high & last post-SE s18 medium to high
62 max relative signal enhancement(rim) medium to high & Variance ptime1 very high & Difference variance ptime2 very low to high
588 SER(in) high & irregularity high
615 irregularity high & 1st post-SE s15 medium to high
10681 Difference variance ptime1 very high & Difference variance ptime2 very low to high
85 Variance ptime1 very high & dispersion s16 medium to high
7286 irregularity medium to high & Variance ptime1 very high & Difference variance ptime4 very low to high & T2w Difference entropy low to very high
155 Variance ptime1 very high & dispersion s16 medium to high
184 SER(in) medium to high & irregularity high
135 SER(in) medium to high & irregularity high
2589 Variance ptime2 very high & Difference variance ptime2 very low to high
511 SER(in) medium to high & irregularity high
454 Time-to-peak(in) low & irregularity medium to high & 1st post-SE s12 medium to high
124 Time-to-peak(in) low & Rate of signal increase(rim) medium to high & irregularity medium to high
pred prob sumtempProb
10957 C 0.5682319, 0.6838746, 0.4879725, 0.4530955, 0.4300886 0.5246526
322 C 0.4675507, 0.7419192 0.604735
420 C 0.4705374, 0.8140437, 0.7544592 0.6796801
68 C 0.4479334, 0.7561858, 0.6379134 0.6140108
9295 C 0.7741849, 0.4788727, 0.7091933 0.6540836
11396 C 0.5191539, 0.4959777, 0.3986381 0.4712566
112 C 0.7075908, 0.4421720 0.5748814
4999 C 0.3727659, 0.5435277, 0.4635614 0.4599517
40 C 0.5017755, 0.7615645 0.63167
670 C 0.5627317, 0.5135349, 0.6720011 0.5827559
310 C 0.5006988, 0.6626664 0.5816826
12068 C 0.4815758, 0.4739428, 0.5346694 0.4967293
2791 C 0.6633012, 0.5110174, 0.6863620 0.6202269
2963 C 0.4627302, 0.4869596, 0.5895322 0.513074
300 C 0.5949279, 0.7518615, 0.4569649 0.6012514
1063 C 0.5128461, 0.6452170, 0.4944342 0.5508324
455 C 0.7662063, 0.4502787 0.6082425
7460 C 0.2956963, 0.4250158, 0.5423104 0.4210075
62 C 0.8237662, 0.4610768, 0.7663881 0.6837437
588 C 0.4565346, 0.6397499 0.5481423
615 C 0.4819968, 0.7471799 0.6145883
10681 C 0.4832205, 0.4638078 0.4735142
85 C 0.4344588, 0.7756773 0.6050681
7286 C 0.7622081, 0.4384610, 0.4232979, 0.4466687 0.5176589
155 C 0.4291609, 0.7692691 0.599215
184 C 0.7579719, 0.4714506 0.6147112
135 C 0.7467186, 0.4575242 0.6021214
2589 C 0.4973411, 0.4768212 0.4870812
511 C 0.7969179, 0.5002271 0.6485725
454 C 0.7569990, 0.5009352, 0.6581838 0.638706
124 C 0.7280304, 0.4252003, 0.5877582 0.5803296
Ruletype
10957 T1wdynamic & T1wmorphology & dispersion
322 T1wmorphology & T1wtexture
420 T1wtexture & dispersion & single-time-Enh
68 T1wdynamic & T1wmorphology
9295 T1wdynamic & T1wmorphology & single-time-Enh
11396 T1wdynamic & T1wtexture
112 T1wmorphology & T1wtexture
4999 T1wdynamic & single-time-Enh & T2w
40 T1wmorphology & T1wtexture
670 T1wmorphology & T1wtexture
310 T1wdynamic & T1wmorphology
12068 T1wmorphology & T1wtexture & dispersion
2791 T1wdynamic & T1wmorphology
2963 T1wdynamic & T1wtexture & single-time-Enh
300 T1wdynamic & T1wmorphology
1063 T1wmorphology & T1wtexture & single-time-Enh
455 T1wdynamic & T1wmorphology
7460 T1wdynamic & T1wmorphology & single-time-Enh
62 T1wdynamic & T1wtexture
588 T1wdynamic & T1wmorphology
615 T1wmorphology & single-time-Enh
10681 T1wtexture
85 T1wtexture & dispersion
7286 T1wmorphology & T1wtexture & T2w
155 T1wtexture & dispersion
184 T1wdynamic & T1wmorphology
135 T1wdynamic & T1wmorphology
2589 T1wtexture
511 T1wdynamic & T1wmorphology
454 T1wdynamic & T1wmorphology & single-time-Enh
124 T1wdynamic & T1wmorphology
# print(IDC[IDC$allTestinfo.lesion_id==241,])
imgIDC <- readPNG(paste0("Z:/Cristina/Section2/papernew_notes/images/", as.character(lesion_id),
"_", infoidx$cad_pt_no_txt, "_", infoidx$exam_a_number_txt, "_", infoidx$lesion_label, "_",
lesioninfo[lesioninfo$lesion_id == lesion_id, "find_t2_signal_int"], ".png"))
grid.raster(imgIDC)
## with LMSIR
if (length(idLMSIR) > 0) {
for (i in 1:length(idLMSIR)) {
idx = idLMSIR[i]
lesion_id = IDC[idx, ]$allTestinfo.lesion_id
print(lesion_id)
}
}
[1] 189
[1] 95
[1] 350
[1] 541
[1] 580
[1] 589
[1] 8
[1] 9
[1] 441
idx = c(1:nrow(IDC))[c(IDC$allTestinfo.lesion_id == lesion_id)]
infoidx = allTestinfo[allTestinfo$lesion_id == lesion_id, -c(20)]
print(infoidx)
lesion_id lesionfile cad_pt_no_txt anony_dob_datetime exam_img_dicom_txt
441 441 441_3053_7449310.vtk 3053 1960-08-21 00:00:00.000000 31654
exam_a_number_txt exam_dt_datetime exam_mri_cad_status_txt
441 7449310 2013-04-07 00:00:00.000000 Unknown
cad_latest_mutation_status_int exam_find_mri_mass_yn exam_find_mri_nonmass_yn
441 None 0 1
exam_find_side_int proc_pt_procedure_id proc_proc_dt_datetime proc_proc_side_int
441 Right 4075 2013-04-23 00:00:00.000000 Right
proc_proc_source_int proc_proc_guid_int proc_proc_tp_int proc_lesion_comments_txt
441 Radiology Stereo Core Needle Biopsy None
find_curve_int find_mri_dce_init_enh_int find_mri_dce_delay_enh_int BIRADS lesion_label
441 None Rapid Washout 5 nonmassM
lesion_diagnosis
441 InvasiveDuctal
print(mypresentRules(eachIDCTopRules[[idx]], colnames(X), fnames))
len freq err
3499 4 0.031 0
4984 2 0.042 0.043
11396 3 0.063 0.0590000000000001
3868 3 0.031 0.0590000000000001
4999 3 0.059 0.0620000000000001
2963 3 0.091 0.08
7460 3 0.062 0.088
condition
3499 max uptake very high & Sum average ptime2 very low to high & last post-SE s8 low to very high & T2w Sum average low to very high
4984 max uptake very high & last post-SE s8 low to very high
11396 Washout rate(in) very high & Sum Entropy ptime1 very high & Entropy ptime1 very high
3868 dispersion s15 low to very high & 3rd post-SE s4 high & predicted LMSIR very low
4999 uptake average high & 1st post-SE s8 high & T2w Correlation low
2963 uptake average high & Energy ptime4 very low to high & last post-SE s2 high
7460 uptake average high & std 3D Sharpness of lesion margin high & last post-SE s18 medium to high
pred prob sumtempProb
3499 C 0.4648681, 0.4791564, 0.4145251, 0.4431299 0.4504199
4984 C 0.5415453, 0.4910949 0.5163201
11396 C 0.5191539, 0.4959777, 0.3986381 0.4712566
3868 C 0.4853810, 0.6962119, 0.4631950 0.5482627
4999 C 0.3727659, 0.5435277, 0.4635614 0.4599517
2963 C 0.4627302, 0.4869596, 0.5895322 0.513074
7460 C 0.2956963, 0.4250158, 0.5423104 0.4210075
Ruletype
3499 T1wdynamic & T1wtexture & single-time-Enh & T2w
4984 T1wdynamic & single-time-Enh
11396 T1wdynamic & T1wtexture
3868 dispersion & single-time-Enh & T2w
4999 T1wdynamic & single-time-Enh & T2w
2963 T1wdynamic & T1wtexture & single-time-Enh
7460 T1wdynamic & T1wmorphology & single-time-Enh
2) Present rules collect top for InsituDuctal ISDC
eachISDCTopRules = list()
allISDCtoprules = c()
for (idx in 1:nrow(ISDC)) {
############## first analysis
X = ISDC[idx, 2:ncol(imgT2pLMSIRtest)]
y = ISDC[idx, "lesion_label"]
rulesoutputISDC = mynewapplyLearnerxrules(topRulesISDC, X, y, minerr = 0.1, minfrq = 10/627,
classes, gbmModel)
topRulesISDC = rulesoutputISDC[[1]]
if (length(rulesoutputISDC) > 1) {
eachISDCTopRules[[idx]] = rulesoutputISDC[[2]]
allISDCtoprules = rbind(allISDCtoprules, rulesoutputISDC[[3]])
} else {
eachISDCTopRules[[idx]] = list()
allISDCtoprules = rbind(allISDCtoprules, 1:nrow(topRulesISDC) * 0)
}
}
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 7 out of 50"
[1] "test complies with # rules: 6 out of 50"
[1] "test complies with # rules: 7 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 15 out of 50"
[1] "test complies with # rules: 13 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 5 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 1 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 6 out of 50"
[1] "test complies with # rules: 11 out of 50"
[1] "test complies with # rules: 9 out of 50"
[1] "test complies with # rules: 6 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 1 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 7 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 1 out of 50"
[1] "test complies with # rules: 1 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 6 out of 50"
[1] "test complies with # rules: 9 out of 50"
[1] "test complies with # rules: 13 out of 50"
[1] "test complies with # rules: 7 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 1 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 9 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 7 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 5 out of 50"
[1] "test complies with # rules: 5 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 14 out of 50"
[1] "test complies with # rules: 6 out of 50"
[1] "test complies with # rules: 10 out of 50"
[1] "test complies with # rules: 5 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 1 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 5 out of 50"
[1] "test complies with # rules: 6 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 7 out of 50"
[1] "test complies with # rules: 6 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 1 out of 50"
[1] "test complies with # rules: 1 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 10 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 14 out of 50"
[1] "test complies with # rules: 10 out of 50"
[1] "test complies with # rules: 10 out of 50"
# take the occurance of each explaining rule (columns) per case(row) + lesion identifies
df = data.frame(cbind(allISDCtoprules, as.character(ISDC$allTestinfo.lesion_id), as.character(ISDC$allTestinfo.lesion_label),
as.character(ISDC$allTestinfo.lesion_diagnosis)), stringsAsFactors = FALSE)
colnames(df) <- c(as.character(1:nrow(topRulesISDC)), "lesion_id", "lesion_label", "lesion_diagnosis")
cols = 1:nrow(topRulesISDC)
df[, cols] = apply(df[, cols], 2, function(x) as.numeric(x))
cat(paste0("\n============== Top five explaining rules for InsituDuctal (ISDC): n = ", nrow(ISDC),
"\n"))
============== Top five explaining rules for InsituDuctal (ISDC): n = 80
topISDC = sort(colSums(df[, 1:nrow(topRulesISDC)]), decreasing = TRUE)
print(topISDC[1:5])
42 50 21 48 41
27 21 20 19 18
freqtopISDC = topISDC[1:5]
print(freqtopISDC/nrow(ISDC))
42 50 21 48 41
0.3375 0.2625 0.2500 0.2375 0.2250
rulesTopISDC = as.numeric(names(topISDC[1:5]))
preserulesTopISDC = mypresentRules(topRulesISDC[rulesTopISDC, ], colnames(X), fnames)
rownames(preserulesTopISDC) <- NULL
print(preserulesTopISDC)
len freq err
1 4 0.159 0.093
2 2 0.152 0.098
3 2 0.135 0.0679999999999999
4 2 0.095 0.096
5 3 0.101 0.091
condition
1 irregularity medium to high & Variance ptime1 very high & Difference variance ptime4 very low to high & T2w Difference entropy low to very high
2 irregularity high & Variance ptime1 high
3 irregularity high & Sum variance ptime1 high
4 Variance ptime2 very high & Difference variance ptime2 very low to high
5 SER(in) medium to high & irregularity high & Difference entropy ptime3 high
pred prob sumtempProb
1 C 0.7622081, 0.4384610, 0.4232979, 0.4466687 0.5176589
2 C 0.4852856, 0.7650575 0.6251715
3 C 0.5087730, 0.8044078 0.6565904
4 C 0.4973411, 0.4768212 0.4870812
5 C 0.4542278, 0.3886270, 0.5466488 0.4631679
Ruletype
1 T1wmorphology & T1wtexture & T2w
2 T1wmorphology & T1wtexture
3 T1wmorphology & T1wtexture
4 T1wtexture
5 T1wdynamic & T1wmorphology & T1wtexture
# display a case that meets them all
casesISDC = df[, c(rulesTopISDC, nrow(topRulesISDC) + 1, nrow(topRulesISDC) + 2, nrow(topRulesISDC) +
3)]
print("Sorted cases meeting top five explaining rules for InsituDuctal (ISDC):")
[1] "Sorted cases meeting top five explaining rules for InsituDuctal (ISDC):"
topcasesISDC = casesISDC[sort(rowSums(casesISDC[, 1:5]), index = TRUE, decreasing = TRUE)$ix, ]
print(topcasesISDC)
42 50 21 48 41 lesion_id lesion_label lesion_diagnosis
9 1 1 1 1 1 294 massM InsituDuctal
10 1 1 1 1 1 295 nonmassM InsituDuctal
31 1 1 1 1 1 395 massM InsituDuctal
32 1 1 1 1 1 612 massM InsituDuctal
45 1 1 1 1 1 246 massM InsituDuctal
59 1 1 1 1 1 564 massM InsituDuctal
7 1 1 1 1 0 466 nonmassM InsituDuctal
16 1 1 1 0 1 571 massM InsituDuctal
41 1 1 1 0 1 551 massM InsituDuctal
57 1 1 1 0 1 562 massM InsituDuctal
76 1 1 1 1 0 595 massM InsituDuctal
78 1 1 1 1 0 608 massM InsituDuctal
79 1 1 1 0 1 609 massM InsituDuctal
80 1 1 1 0 1 610 nonmassM InsituDuctal
13 0 1 1 0 1 359 nonmassM InsituDuctal
38 0 1 1 0 1 454 nonmassM InsituDuctal
40 0 1 1 0 1 550 nonmassM InsituDuctal
46 1 0 0 1 1 340 massM InsituDuctal
69 0 1 1 0 1 402 massM InsituDuctal
72 0 1 1 1 0 581 nonmassM InsituDuctal
3 1 0 0 1 0 232 nonmassM InsituDuctal
6 0 1 1 0 0 416 nonmassM InsituDuctal
18 1 0 0 1 0 573 massM InsituDuctal
19 1 0 0 1 0 574 massM InsituDuctal
20 1 0 0 1 0 575 massM InsituDuctal
37 1 0 0 1 0 382 massM InsituDuctal
58 1 0 0 1 0 563 massM InsituDuctal
60 1 0 0 1 0 565 massM InsituDuctal
70 1 0 0 1 0 459 massM InsituDuctal
5 0 1 0 0 0 414 nonmassM InsituDuctal
11 1 0 0 0 0 296 nonmassM InsituDuctal
17 1 0 0 0 0 572 massM InsituDuctal
25 0 0 0 0 1 198 nonmassM InsituDuctal
64 1 0 0 0 0 170 massM InsituDuctal
68 0 0 0 0 1 376 nonmassM InsituDuctal
71 1 0 0 0 0 460 massM InsituDuctal
1 0 0 0 0 0 1 nonmassM InsituDuctal
2 0 0 0 0 0 134 nonmassM InsituDuctal
4 0 0 0 0 0 285 massM InsituDuctal
8 0 0 0 0 0 250 nonmassM InsituDuctal
12 0 0 0 0 0 300 nonmassM InsituDuctal
14 0 0 0 0 0 374 nonmassM InsituDuctal
15 0 0 0 0 0 458 nonmassM InsituDuctal
21 0 0 0 0 0 33 massM InsituDuctal
22 0 0 0 0 0 34 nonmassM InsituDuctal
23 0 0 0 0 0 83 nonmassM InsituDuctal
24 0 0 0 0 0 133 nonmassM InsituDuctal
26 0 0 0 0 0 318 massM InsituDuctal
27 0 0 0 0 0 118 nonmassM InsituDuctal
28 0 0 0 0 0 138 nonmassM InsituDuctal
29 0 0 0 0 0 195 nonmassM InsituDuctal
30 0 0 0 0 0 316 nonmassM InsituDuctal
33 0 0 0 0 0 69 nonmassM InsituDuctal
34 0 0 0 0 0 184 massM InsituDuctal
35 0 0 0 0 0 275 massM InsituDuctal
36 0 0 0 0 0 381 nonmassM InsituDuctal
39 0 0 0 0 0 549 massM InsituDuctal
42 0 0 0 0 0 131 massM InsituDuctal
43 0 0 0 0 0 132 nonmassM InsituDuctal
44 0 0 0 0 0 173 massM InsituDuctal
47 0 0 0 0 0 365 massM InsituDuctal
48 0 0 0 0 0 531 nonmassM InsituDuctal
49 0 0 0 0 0 113 nonmassM InsituDuctal
50 0 0 0 0 0 164 nonmassM InsituDuctal
51 0 0 0 0 0 483 nonmassM InsituDuctal
52 0 0 0 0 0 606 nonmassM InsituDuctal
53 0 0 0 0 0 129 massM InsituDuctal
54 0 0 0 0 0 218 massM InsituDuctal
55 0 0 0 0 0 234 massM InsituDuctal
56 0 0 0 0 0 277 massM InsituDuctal
61 0 0 0 0 0 5 nonmassM InsituDuctal
62 0 0 0 0 0 30 massM InsituDuctal
63 0 0 0 0 0 120 massM InsituDuctal
65 0 0 0 0 0 268 nonmassM InsituDuctal
66 0 0 0 0 0 298 nonmassM InsituDuctal
67 0 0 0 0 0 375 massM InsituDuctal
73 0 0 0 0 0 37 nonmassM InsituDuctal
74 0 0 0 0 0 140 nonmassM InsituDuctal
75 0 0 0 0 0 464 nonmassM InsituDuctal
77 0 0 0 0 0 596 massM InsituDuctal
print("Fine explaining rules for InsituDuctal (ISDC) with LMSIR:")
[1] "Fine explaining rules for InsituDuctal (ISDC) with LMSIR:"
LMSIRfeatureflag = c()
idLMSIR = c()
for (i in 1:length(eachISDCTopRules)) {
if (length(eachISDCTopRules[[i]]) > 0) {
rules = mypresentRules(eachISDCTopRules[[i]], colnames(X), fnames)
LMSIRwtop5 = "LMSIR" %in% unlist(strsplit(unlist(strsplit(rules$condition, split = " & ")),
split = " "))
if (LMSIRwtop5) {
LMSIRfeatureflag = c(LMSIRfeatureflag, LMSIRwtop5)
print(i)
print(rules)
idLMSIR = c(idLMSIR, i)
} else {
LMSIRfeatureflag = c(LMSIRfeatureflag, FALSE)
}
} else {
LMSIRfeatureflag = c(LMSIRfeatureflag, FALSE)
}
}
[1] 2
len freq err
4715 4 0.027 0
6488 3 0.102 0.036
13591 4 0.09 0.0610000000000001
condition
4715 2nd post-SE s18 low to very high & 3rd post-SE s4 high & last post-SE s8 low to very high & predicted LMSIR very low
6488 Time-to-peak(in) medium to high & uptake skewness low & irregularity very low
13591 enhancement-variance decreasing rate(rim) very low to high & irregularity low & Sum average ptime1 high & 2nd post-SE s14 very low to high
pred prob sumtempProb
4715 C 0.5430140, 0.7717451, 0.5008960, 0.5124503 0.5820264
6488 NC 0.4742468, 0.3732442, 0.4938563 0.4471158
13591 NC 0.4442097, 0.5323714, 0.4614969, 0.5905932 0.5071678
Ruletype
4715 single-time-Enh & T2w
6488 T1wdynamic & T1wmorphology
13591 T1wdynamic & T1wmorphology & T1wtexture & single-time-Enh
[1] 27
len freq err
4715 4 0.027 0
593 2 0.248 0.096
condition
4715 2nd post-SE s18 low to very high & 3rd post-SE s4 high & last post-SE s8 low to very high & predicted LMSIR very low
593 SER(in) low & max Radial gradient medium to high
pred prob sumtempProb Ruletype
4715 C 0.5430140, 0.7717451, 0.5008960, 0.5124503 0.5820264 single-time-Enh & T2w
593 NC 0.5088292, 0.2628051 0.3858172 T1wdynamic & T1wmorphology
[1] 33
len freq err
4715 4 0.027 0
13591 4 0.09 0.0610000000000001
442 3 0.237 0.07
478 3 0.156 0.093
condition
4715 2nd post-SE s18 low to very high & 3rd post-SE s4 high & last post-SE s8 low to very high & predicted LMSIR very low
13591 enhancement-variance decreasing rate(rim) very low to high & irregularity low & Sum average ptime1 high & 2nd post-SE s14 very low to high
442 irregularity low & Variance ptime2 low to medium & Energy ptime4 very low to high
478 irregularity low & std 3D Sharpness of lesion margin medium to high & Inverse difference moment ptime3 low to medium
pred prob sumtempProb
4715 C 0.5430140, 0.7717451, 0.5008960, 0.5124503 0.5820264
13591 NC 0.4442097, 0.5323714, 0.4614969, 0.5905932 0.5071678
442 NC 0.4378788, 0.2352466, 0.2721108 0.3150787
478 NC 0.5702187, 0.4669343, 0.3339196 0.4570242
Ruletype
4715 single-time-Enh & T2w
13591 T1wdynamic & T1wmorphology & T1wtexture & single-time-Enh
442 T1wmorphology & T1wtexture
478 T1wmorphology & T1wtexture
[1] 52
len freq err
4715 4 0.027 0
9188 5 0.038 0.048
715 3 0.08 0.0679999999999999
442 3 0.237 0.07
2980 3 0.076 0.071
4592 2 0.091 0.082
2203 3 0.093 0.098
condition
4715 2nd post-SE s18 low to very high & 3rd post-SE s4 high & last post-SE s8 low to very high & predicted LMSIR very low
9188 max uptake medium to high & Entropy ptime2 low to very high & 1st post-SE s16 low to medium & 3rd post-SE s10 low to very high & T2w Difference variance very low
715 uptake average high & Inverse difference moment ptime2 low to medium & 1st post-SE s8 high
442 irregularity low & Variance ptime2 low to medium & Energy ptime4 very low to high
2980 uptake average high & 1st post-SE s8 high & last post-SE s11 high
4592 uptake average high & 2nd post-SE s2 high
2203 uptake average high & Inverse difference moment ptime2 low to medium & 1st post-SE s8 high
pred prob sumtempProb
4715 C 0.5430140, 0.7717451, 0.5008960, 0.5124503 0.5820264
9188 NC 0.4555243, 0.4955115, 0.5378557, 0.4726280, 0.4208891 0.4764817
715 C 0.5436611, 0.6397459, 0.5003391 0.5612487
442 NC 0.4378788, 0.2352466, 0.2721108 0.3150787
2980 C 0.5757935, 0.5294741, 0.6741425 0.5931367
4592 C 0.4996731, 0.5976669 0.54867
2203 C 0.5260448, 0.6336959, 0.5132996 0.5576801
Ruletype
4715 single-time-Enh & T2w
9188 T1wdynamic & T1wtexture & single-time-Enh & T2w
715 T1wdynamic & T1wtexture & single-time-Enh
442 T1wmorphology & T1wtexture
2980 T1wdynamic & single-time-Enh
4592 T1wdynamic & single-time-Enh
2203 T1wdynamic & T1wtexture & single-time-Enh
[1] 73
len freq err
4715 4 0.027 0
condition
4715 2nd post-SE s18 low to very high & 3rd post-SE s4 high & last post-SE s8 low to very high & predicted LMSIR very low
pred prob sumtempProb Ruletype
4715 C 0.5430140, 0.7717451, 0.5008960, 0.5124503 0.5820264 single-time-Enh & T2w
[1] 74
len freq err
4715 4 0.027 0
condition
4715 2nd post-SE s18 low to very high & 3rd post-SE s4 high & last post-SE s8 low to very high & predicted LMSIR very low
pred prob sumtempProb Ruletype
4715 C 0.5430140, 0.7717451, 0.5008960, 0.5124503 0.5820264 single-time-Enh & T2w
print(summary(LMSIRfeatureflag))
Mode FALSE TRUE NA's
logical 74 6 0
### display
lesion_id = 595
idx = c(1:nrow(ISDC))[c(ISDC$allTestinfo.lesion_id == lesion_id)]
infoidx = allTestinfo[allTestinfo$lesion_id == lesion_id, -c(20)]
print(infoidx)
lesion_id lesionfile cad_pt_no_txt anony_dob_datetime exam_img_dicom_txt
595 595 595_7018_6803089.vtk 7018 1956-11-07 00:00:00.000000 17969
exam_a_number_txt exam_dt_datetime exam_mri_cad_status_txt
595 6803089 2011-05-24 00:00:00.000000 Malignant
cad_latest_mutation_status_int exam_find_mri_mass_yn exam_find_mri_nonmass_yn
595 None 1 0
exam_find_side_int proc_pt_procedure_id proc_proc_dt_datetime proc_proc_side_int
595 Right 3315 2012-04-26 00:00:00.000000 Right
proc_proc_source_int proc_proc_guid_int proc_proc_tp_int
595 Radiology US Core Needle Biopsy
proc_lesion_comments_txt
595 CLINICAL INDICATION: Suspicious segmental microcalcifications on the mammogram
find_curve_int find_mri_dce_init_enh_int find_mri_dce_delay_enh_int BIRADS lesion_label
595 None N/A Plateau 4 massM
lesion_diagnosis
595 InsituDuctal
cat(allTestinfo[allTestinfo$lesion_id == lesion_id, c(20)])
ULTRASOUND GUIDED CORE BIOPSY RIGHT BREAST
CLINICAL HISTORY: suspicious for recurrence medial right breast 3 o'clock 2 cm from nipple
PROCEDURE:
Targeted ultrasound was obtained and the previously described abnormality was identified.
Following informed consent and using sterile technique and local anaesthesia (1% xylocaine), core biopsies were obtained with ultrasound guidance using a ML approach. A skin incision was made and cores were obtained with a 14 gauge tru-cut needle in
an automated gun. Through the same incision several passes were made in order to sample different areas. 4 cores were obtained.
There were no immediate complications. The patient was given a sheet of post biopsy instructions.
The patient was requested to contact her referring physician for the results.
CORE PATHOLOGY: highly suspicious for ductal carcinoma in situ. This result is concordant.
MRI is recommended for further assessment.
_____________
This report was electronically signed by WRIGHT, BARBARA, Staff Radiologist on 2012/05/03 at 17:26
--- Addendum ---
ADDENDUM:
This case was discussed at breast multidisciplinary rounds May 31, 2012. Repeat stereotactic guided biopsy with vacuum assistance has been recommended to try to obtain a larger sample of tissue and confirm a diagnosis of DCIS definitively prior to
planning surgical treatment.
This addendum was electronically signed by HACK, KALESHA, Staff Radiologist on 2012/06/01 at 11:28
--- Addendum end ---
print(mypresentRules(eachISDCTopRules[[idx]], colnames(X), fnames))
len freq err
5728 3 0.05 0.037
8280 4 0.035 0.053
90 2 0.135 0.0679999999999999
670 3 0.079 0.07
6675 3 0.087 0.085
4150 5 0.104 0.089
7286 4 0.159 0.093
135 2 0.115 0.095
2589 2 0.095 0.096
315 2 0.152 0.098
condition
5728 uptake variance very high & last post-SE s6 low to very high & T2w Energy low
8280 Rate of signal decrease(in) high & uptake variance very high & circularity low & last post-SE s8 medium to high
90 irregularity high & Sum variance ptime1 high
670 irregularity high & Variance ptime2 high & Sum Entropy ptime2 very high
6675 Sum variance ptime1 high & Inverse difference moment ptime4 medium to high & dispersion s2 medium to high
4150 uptake average high & Max Radial gradient variance low to very high & Energy ptime4 very low to high & dispersion s19 medium to high & 1st post-SE s12 medium to high
7286 irregularity medium to high & Variance ptime1 very high & Difference variance ptime4 very low to high & T2w Difference entropy low to very high
135 SER(in) medium to high & irregularity high
2589 Variance ptime2 very high & Difference variance ptime2 very low to high
315 irregularity high & Variance ptime1 high
pred prob sumtempProb
5728 C 0.7332721, 0.4739669, 0.5252209 0.5774866
8280 C 0.4768186, 0.4505621, 0.7410536, 0.6456018 0.578509
90 C 0.5087730, 0.8044078 0.6565904
670 C 0.5627317, 0.5135349, 0.6720011 0.5827559
6675 C 0.3978654, 0.7406423, 0.5150453 0.5511844
4150 C 0.5303059, 0.5125338, 0.5635975, 0.6702745, 0.6316332 0.581669
7286 C 0.7622081, 0.4384610, 0.4232979, 0.4466687 0.5176589
135 C 0.7467186, 0.4575242 0.6021214
2589 C 0.4973411, 0.4768212 0.4870812
315 C 0.4852856, 0.7650575 0.6251715
Ruletype
5728 T1wdynamic & single-time-Enh & T2w
8280 T1wdynamic & T1wmorphology & single-time-Enh
90 T1wmorphology & T1wtexture
670 T1wmorphology & T1wtexture
6675 T1wtexture & dispersion
4150 T1wdynamic & T1wmorphology & T1wtexture & dispersion & single-time-Enh
7286 T1wmorphology & T1wtexture & T2w
135 T1wdynamic & T1wmorphology
2589 T1wtexture
315 T1wmorphology & T1wtexture
# print(ISDC[ISDC$allTestinfo.lesion_id==241,])
imgISDC <- readPNG(paste0("Z:/Cristina/Section2/papernew_notes/images/", as.character(lesion_id),
"_", infoidx$cad_pt_no_txt, "_", infoidx$exam_a_number_txt, "_", infoidx$lesion_label, "_",
lesioninfo[lesioninfo$lesion_id == lesion_id, "find_t2_signal_int"], ".png"))
grid.raster(imgISDC)
## with LMSIR
if (length(idLMSIR) > 0) {
for (i in 1:length(idLMSIR)) {
idx = idLMSIR[i]
lesion_id = ISDC[idx, ]$allTestinfo.lesion_id
print(lesion_id)
}
}
[1] 134
[1] 118
[1] 69
[1] 606
[1] 37
[1] 140
idx = c(1:nrow(ISDC))[c(ISDC$allTestinfo.lesion_id == lesion_id)]
infoidx = allTestinfo[allTestinfo$lesion_id == lesion_id, -c(20)]
print(infoidx)
lesion_id lesionfile cad_pt_no_txt anony_dob_datetime exam_img_dicom_txt
140 140 140_0684_5266209.vtk 0684 1956-10-14 00:00:00.000000 12766
exam_a_number_txt exam_dt_datetime exam_mri_cad_status_txt
140 5266209 2010-07-24 00:00:00.000000 Malignant
cad_latest_mutation_status_int exam_find_mri_mass_yn exam_find_mri_nonmass_yn
140 High Risk 0 1
exam_find_side_int proc_pt_procedure_id proc_proc_dt_datetime proc_proc_side_int
140 Right 173 2010-08-05 00:00:00.000000 Right
proc_proc_source_int proc_proc_guid_int proc_proc_tp_int
140 Radiology US Core Needle Biopsy
proc_lesion_comments_txt
140 Life time risk > 25%. Left lumpectomy for ADH in\n2004. Family history of breast cancer. LMP: Early June 2010.\n
find_curve_int find_mri_dce_init_enh_int find_mri_dce_delay_enh_int BIRADS lesion_label
140 None N/A N/A 4 nonmassM
lesion_diagnosis
140 InsituDuctal
print(mypresentRules(eachISDCTopRules[[idx]], colnames(X), fnames))
len freq err
4715 4 0.027 0
condition
4715 2nd post-SE s18 low to very high & 3rd post-SE s4 high & last post-SE s8 low to very high & predicted LMSIR very low
pred prob sumtempProb Ruletype
4715 C 0.5430140, 0.7717451, 0.5008960, 0.5124503 0.5820264 single-time-Enh & T2w
3) Present rules collect top for FIBROADENOMA FA
eachFATopRules = list()
allFAtoprules = c()
for (idx in 1:nrow(FA)) {
############## first analysis
X = FA[idx, 2:ncol(imgT2pLMSIRtest)]
y = FA[idx, "lesion_label"]
rulesoutputFA = mynewapplyLearnerxrules(topRulesFA, X, y, minerr = 0.1, minfrq = 10/627, classes,
gbmModel)
topRulesFA = rulesoutputFA[[1]]
if (length(rulesoutputFA) > 1) {
eachFATopRules[[idx]] = rulesoutputFA[[2]]
allFAtoprules = rbind(allFAtoprules, rulesoutputFA[[3]])
} else {
eachFATopRules[[idx]] = list()
allFAtoprules = rbind(allFAtoprules, 1:nrow(topRulesFA) * 0)
}
}
[1] "test complies with # rules: 16 out of 50"
[1] "test complies with # rules: 1 out of 50"
[1] "test complies with # rules: 11 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 14 out of 50"
[1] "test complies with # rules: 6 out of 50"
[1] "test complies with # rules: 11 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 19 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 5 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 21 out of 50"
[1] "test complies with # rules: 5 out of 50"
[1] "test complies with # rules: 23 out of 50"
[1] "test complies with # rules: 16 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 13 out of 50"
[1] "test complies with # rules: 14 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 11 out of 50"
[1] "test complies with # rules: 24 out of 50"
[1] "test complies with # rules: 24 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 11 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 24 out of 50"
[1] "test complies with # rules: 20 out of 50"
[1] "test complies with # rules: 12 out of 50"
[1] "test complies with # rules: 9 out of 50"
[1] "test complies with # rules: 20 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 18 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 14 out of 50"
[1] "test complies with # rules: 17 out of 50"
[1] "test complies with # rules: 5 out of 50"
[1] "test complies with # rules: 12 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 24 out of 50"
[1] "test complies with # rules: 27 out of 50"
[1] "test complies with # rules: 20 out of 50"
[1] "test complies with # rules: 15 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 6 out of 50"
[1] "test complies with # rules: 6 out of 50"
[1] "test complies with # rules: 16 out of 50"
[1] "test complies with # rules: 18 out of 50"
[1] "test complies with # rules: 26 out of 50"
[1] "test complies with # rules: 11 out of 50"
[1] "test complies with # rules: 12 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 5 out of 50"
[1] "test complies with # rules: 9 out of 50"
[1] "test complies with # rules: 12 out of 50"
[1] "test complies with # rules: 7 out of 50"
[1] "test complies with # rules: 11 out of 50"
[1] "test complies with # rules: 20 out of 50"
[1] "test complies with # rules: 17 out of 50"
[1] "test complies with # rules: 14 out of 50"
[1] "test complies with # rules: 1 out of 50"
[1] "test complies with # rules: 9 out of 50"
[1] "test complies with # rules: 7 out of 50"
[1] "test complies with # rules: 6 out of 50"
# take the occurance of each explaining rule (columns) per case(row) + lesion identifies
df = data.frame(cbind(allFAtoprules, as.character(FA$allTestinfo.lesion_id), as.character(FA$allTestinfo.lesion_label),
as.character(FA$allTestinfo.lesion_diagnosis)), stringsAsFactors = FALSE)
colnames(df) <- c(as.character(1:nrow(topRulesFA)), "lesion_id", "lesion_label", "lesion_diagnosis")
cols = 1:nrow(topRulesFA)
df[, cols] = apply(df[, cols], 2, function(x) as.numeric(x))
cat(paste0("\n============== Top five explaining rules for FIBROADENOMA (FA): n = ", nrow(FA) +
1, "\n"))
============== Top five explaining rules for FIBROADENOMA (FA): n = 70
topFA = sort(colSums(df[, 1:nrow(topRulesFA)]), decreasing = TRUE)
print(topFA[1:5])
28 35 26 30 32
32 32 28 28 28
freqtopFA = topFA[1:5]
totalFA = nrow(FA) + 1
print(freqtopFA/totalFA)
28 35 26 30 32
0.4571429 0.4571429 0.4000000 0.4000000 0.4000000
rulesTopFA = as.numeric(names(topFA[1:5]))
preserulesTopFA = mypresentRules(topRulesFA[rulesTopFA, ], colnames(X), fnames)
rownames(preserulesTopFA) <- NULL
print(preserulesTopFA)
len freq err
1 2 0.228 0.072
2 2 0.246 0.081
3 3 0.237 0.07
4 2 0.2 0.073
5 2 0.193 0.077
condition pred
1 SER(in) low to medium & irregularity low NC
2 SER(in) low to medium & irregularity low NC
3 irregularity low & Variance ptime2 low to medium & Energy ptime4 very low to high NC
4 irregularity low & Energy ptime4 low to medium NC
5 irregularity low & Energy ptime4 low to medium NC
prob sumtempProb Ruletype
1 0.4405761, 0.3043518 0.372464 T1wdynamic & T1wmorphology
2 0.5053493, 0.3706932 0.4380213 T1wdynamic & T1wmorphology
3 0.4378788, 0.2352466, 0.2721108 0.3150787 T1wmorphology & T1wtexture
4 0.4867494, 0.2974405 0.392095 T1wmorphology & T1wtexture
5 0.4991863, 0.2996197 0.399403 T1wmorphology & T1wtexture
# display a case that meets them all
casesFA = df[, c(rulesTopFA, nrow(topRulesFA) + 1, nrow(topRulesFA) + 2, nrow(topRulesFA) + 3)]
print("Sorted cases meeting top five explaining rules for FIBROADENOMA (FA):")
[1] "Sorted cases meeting top five explaining rules for FIBROADENOMA (FA):"
topcasesFA = casesFA[sort(rowSums(casesFA[, 1:5]), index = TRUE, decreasing = TRUE)$ix, ]
print(topcasesFA)
28 35 26 30 32 lesion_id lesion_label lesion_diagnosis
1 1 1 1 1 1 104 massB FIBROADENOMA
9 1 1 1 1 1 112 massB FIBROADENOMA
14 1 1 1 1 1 436 massB FIBROADENOMA
16 1 1 1 1 1 592 massB FIBROADENOMA
17 1 1 1 1 1 604 massB FIBROADENOMA
23 1 1 1 1 1 326 massB FIBROADENOMA
24 1 1 1 1 1 408 massB FIBROADENOMA
28 1 1 1 1 1 377 nonmassB FIBROADENOMA
35 1 1 1 1 1 425 massB FIBROADENOMA
37 1 1 1 1 1 73 massB FIBROADENOMA
45 1 1 1 1 1 366 massB FIBROADENOMA
46 1 1 1 1 1 78 massB FIBROADENOMA
52 1 1 1 1 1 272 massB FIBROADENOMA
53 1 1 1 1 1 618 massB FIBROADENOMA
54 1 1 1 1 1 49 massB FIBROADENOMA
63 1 1 1 1 1 151 massB FIBROADENOMA
64 1 1 1 1 1 310 massB FIBROADENOMA
30 1 1 0 1 1 502 massB FIBROADENOMA
33 1 1 0 1 1 584 massB FIBROADENOMA
38 1 1 0 1 1 100 massB FIBROADENOMA
47 1 1 0 1 1 167 nonmassB FIBROADENOMA
5 1 1 1 0 0 535 massB FIBROADENOMA
7 0 0 1 1 1 55 massB FIBROADENOMA
19 0 0 1 1 1 616 massB FIBROADENOMA
20 1 1 1 0 0 127 massB FIBROADENOMA
22 1 1 1 0 0 325 massB FIBROADENOMA
26 1 1 1 0 0 601 massB FIBROADENOMA
32 1 1 1 0 0 583 massB FIBROADENOMA
55 0 0 1 1 1 60 massB FIBROADENOMA
56 0 0 1 1 1 61 massB FIBROADENOMA
60 1 1 1 0 0 439 massB FIBROADENOMA
3 0 0 0 1 1 378 massB FIBROADENOMA
31 0 0 0 1 1 517 massB FIBROADENOMA
36 1 1 0 0 0 36 nonmassB FIBROADENOMA
40 1 1 0 0 0 130 massB FIBROADENOMA
48 0 0 0 1 1 208 massB FIBROADENOMA
62 1 1 0 0 0 53 massB FIBROADENOMA
65 1 1 0 0 0 314 nonmassB FIBROADENOMA
67 1 1 0 0 0 467 massB FIBROADENOMA
49 0 0 1 0 0 18 nonmassB FIBROADENOMA
2 0 0 0 0 0 309 massB FIBROADENOMA
4 0 0 0 0 0 534 massB FIBROADENOMA
6 0 0 0 0 0 536 massB FIBROADENOMA
8 0 0 0 0 0 90 massB FIBROADENOMA
10 0 0 0 0 0 323 nonmassB FIBROADENOMA
11 0 0 0 0 0 327 massB FIBROADENOMA
12 0 0 0 0 0 373 massB FIBROADENOMA
13 0 0 0 0 0 435 massB FIBROADENOMA
15 0 0 0 0 0 437 massB FIBROADENOMA
18 0 0 0 0 0 615 massB FIBROADENOMA
21 0 0 0 0 0 304 massB FIBROADENOMA
25 0 0 0 0 0 597 massB FIBROADENOMA
27 0 0 0 0 0 635 nonmassB FIBROADENOMA
29 0 0 0 0 0 501 massB FIBROADENOMA
34 0 0 0 0 0 345 massB FIBROADENOMA
39 0 0 0 0 0 125 massB FIBROADENOMA
41 0 0 0 0 0 174 massB FIBROADENOMA
42 0 0 0 0 0 176 massB FIBROADENOMA
43 0 0 0 0 0 342 massB FIBROADENOMA
44 0 0 0 0 0 343 nonmassB FIBROADENOMA
50 0 0 0 0 0 224 massB FIBROADENOMA
51 0 0 0 0 0 271 massB FIBROADENOMA
57 0 0 0 0 0 157 massB FIBROADENOMA
58 0 0 0 0 0 349 nonmassB FIBROADENOMA
59 0 0 0 0 0 431 massB FIBROADENOMA
61 0 0 0 0 0 496 massB FIBROADENOMA
66 0 0 0 0 0 336 massB FIBROADENOMA
68 0 0 0 0 0 522 nonmassB FIBROADENOMA
69 0 0 0 0 0 629 massB FIBROADENOMA
print("Fine explaining rules for FIBROADENOMA (FA) with LMSIR:")
[1] "Fine explaining rules for FIBROADENOMA (FA) with LMSIR:"
LMSIRfeatureflag = c()
idLMSIR = c()
for (i in 1:length(eachFATopRules)) {
if (length(eachFATopRules[[i]]) > 0) {
rules = mypresentRules(eachFATopRules[[i]], colnames(X), fnames)
LMSIRwtop5 = "LMSIR" %in% unlist(strsplit(unlist(strsplit(rules$condition, split = " & ")),
split = " "))
if (LMSIRwtop5) {
LMSIRfeatureflag = c(LMSIRfeatureflag, LMSIRwtop5)
print(i)
print(rules)
idLMSIR = c(idLMSIR, i)
} else {
LMSIRfeatureflag = c(LMSIRfeatureflag, FALSE)
}
} else {
LMSIRfeatureflag = c(LMSIRfeatureflag, FALSE)
}
}
print(summary(LMSIRfeatureflag))
Mode FALSE NA's
logical 69 0
### display
lesion_id = 436
idx = c(1:nrow(FA))[c(FA$allTestinfo.lesion_id == lesion_id)]
infoidx = allTestinfo[allTestinfo$lesion_id == lesion_id, -c(20)]
print(infoidx)
lesion_id lesionfile cad_pt_no_txt anony_dob_datetime exam_img_dicom_txt
436 436 436_3046_7289130.vtk 3046 1970-11-16 00:00:00.000000 29427
exam_a_number_txt exam_dt_datetime exam_mri_cad_status_txt
436 7289130 2012-12-22 00:00:00.000000 Benign by pathology
cad_latest_mutation_status_int exam_find_mri_mass_yn exam_find_mri_nonmass_yn
436 None 1 0
exam_find_side_int proc_pt_procedure_id proc_proc_dt_datetime proc_proc_side_int
436 Right 2691 2013-01-22 00:00:00.000000 Right
proc_proc_source_int proc_proc_guid_int proc_proc_tp_int proc_lesion_comments_txt
436 Radiology US Core Needle Biopsy None
find_curve_int find_mri_dce_init_enh_int find_mri_dce_delay_enh_int BIRADS lesion_label
436 None N/A N/A 4 massB
lesion_diagnosis
436 FIBROADENOMA
cat(allTestinfo[allTestinfo$lesion_id == lesion_id, c(20)])
AP Report:
(NOTE)
SURGICAL PATHOLOGY REPORT
Encounter #: 2695007R
Submitting Physician: MESSNER,SANDRA
Specimen #: S13-1891
CLINICAL INFORMATION
MRI lesion with slight enhancement, hypoechoic on ultrasound - 1cm.
?Fibroadenoma - family history of breast cancer.
SPECIMENS SUBMITTED
Right breast 1 oclock x4 cores
DIAGNOSIS
Right breast 1 oclock x4 cores: FIBROADENOMA, SEE NOTE.
Note: Sections show benign fibroepithelial lesion with mildly
increased stromal cellularity, no cytologic atypia and absent mitoses,
most consistent with a fibroadenoma in this material.
MACROSCOPIC DESCRIPTION
The specimen container is labeled with the patient name and 'right
breast core biopsy'. The accompanying requisition matches the
container's label. The specimen consists of 4 cores of tan and fatty
tissue, each with a diameter of 0.1 cm, ranging from 0.6 to 1.3 cm in
length. Submitted in toto in one block
JP
Dictated 01/24/2013
Elzbieta Slodkowska, MD
Report Electronically Signed
2013/01/25 17:00
print(mypresentRules(eachFATopRules[[idx]], colnames(X), fnames))
len freq err
6093 6 0.031 0
12940 4 0.049 0
519 2 0.176 0.053
1581 3 0.096 0.0570000000000001
459 2 0.064 0.0570000000000001
1541 2 0.162 0.0570000000000001
1996 2 0.184 0.069
331 3 0.106 0.07
442 3 0.237 0.07
3987 5 0.078 0.071
411 2 0.228 0.072
766 2 0.2 0.073
515 4 0.195 0.074
1338 2 0.193 0.077
183 2 0.232 0.079
336 2 0.246 0.081
11043 3 0.111 0.082
1128 2 0.215 0.085
1538 4 0.085 0.087
2330 3 0.216 0.093
722 4 0.136 0.095
condition
6093 SER(in) low to medium & Variance of spatial Margin Gradient low to very high & std 3D Sharpness of lesion margin low to medium & Inverse difference moment ptime4 medium to high & 2nd post-SE s12 very low & 2nd post-SE s17 low to medium
12940 Uptake(in) curve amplitude medium to high & SER(in) low to medium & Variance ptime3 low to medium & dispersion s11 very low
519 irregularity low & Energy ptime4 low to medium
1581 Difference variance ptime1 low & dispersion s16 low to medium & T2w margin gradient low
459 irregularity very low & dispersion s9 medium to high
1541 irregularity low & Energy ptime4 low to medium
1996 irregularity low & Energy ptime4 low to medium
331 SER(in) medium to high & irregularity low & Energy ptime4 low to medium
442 irregularity low & Variance ptime2 low to medium & Energy ptime4 very low to high
3987 Inverse difference moment ptime1 very low to high & dispersion s5 low to very high & dispersion s7 low to very high & 1st post-SE s19 low to very high & 3rd post-SE s12 very low
411 SER(in) low to medium & irregularity low
766 irregularity low & Energy ptime4 low to medium
515 SER(in) low & max Radial gradient medium to high & Sum variance ptime2 very low to high & 1st post-SE s10 low to very high
1338 irregularity low & Energy ptime4 low to medium
183 irregularity low & Inverse difference moment ptime4 low to medium
336 SER(in) low to medium & irregularity low
11043 Sum Entropy ptime1 low to medium & 1st post-SE s8 low to medium & last post-SE s17 high
1128 irregularity low & Energy ptime4 low to medium
1538 Uptake(in) curve amplitude medium to high & Sum Entropy ptime4 low to medium & dispersion s17 low to very high & 3rd post-SE s4 low
2330 irregularity low & Energy ptime3 low to medium & dispersion s5 low to very high
722 uptake average high & irregularity low to medium & 1st post-SE s8 low to medium & T2w radial gradient variance low
pred prob sumtempProb
6093 NC 0.6855391, 0.5934397, 0.5476637, 0.4856720, 0.6810844, 0.5714698 0.5941448
12940 NC 0.4874018, 0.5424656, 0.3437655, 0.4102728 0.4459764
519 NC 0.4703946, 0.2461935 0.358294
1581 NC 0.5724939, 0.3448565, 0.4659352 0.4610952
459 NC 0.6755135, 0.4776196 0.5765665
1541 NC 0.4792871, 0.2735542 0.3764207
1996 NC 0.5007048, 0.3009807 0.4008427
331 NC 0.4648444, 0.5897234, 0.3071130 0.4538936
442 NC 0.4378788, 0.2352466, 0.2721108 0.3150787
3987 NC 0.5232709, 0.5661026, 0.5040197, 0.5410826, 0.4760760 0.5221104
411 NC 0.4405761, 0.3043518 0.372464
766 NC 0.4867494, 0.2974405 0.392095
515 NC 0.2902278, 0.4509106, 0.3336921, 0.3700841 0.3612286
1338 NC 0.4991863, 0.2996197 0.399403
183 NC 0.4863329, 0.2652150 0.3757739
336 NC 0.5053493, 0.3706932 0.4380213
11043 NC 0.4335317, 0.4984163, 0.3944782 0.4421421
1128 NC 0.4553747, 0.2413562 0.3483655
1538 NC 0.6057217, 0.5218727, 0.4647596, 0.4578509 0.5125512
2330 NC 0.4678680, 0.2644552, 0.4902931 0.4075388
722 NC 0.4364043, 0.5007630, 0.5571853, 0.4727589 0.4917779
Ruletype
6093 T1wdynamic & T1wmorphology & T1wtexture & single-time-Enh
12940 T1wdynamic & T1wtexture & dispersion
519 T1wmorphology & T1wtexture
1581 T1wtexture & dispersion & T2w
459 T1wmorphology & dispersion
1541 T1wmorphology & T1wtexture
1996 T1wmorphology & T1wtexture
331 T1wdynamic & T1wmorphology & T1wtexture
442 T1wmorphology & T1wtexture
3987 T1wtexture & dispersion & single-time-Enh
411 T1wdynamic & T1wmorphology
766 T1wmorphology & T1wtexture
515 T1wdynamic & T1wmorphology & T1wtexture & single-time-Enh
1338 T1wmorphology & T1wtexture
183 T1wmorphology & T1wtexture
336 T1wdynamic & T1wmorphology
11043 T1wtexture & single-time-Enh
1128 T1wmorphology & T1wtexture
1538 T1wdynamic & T1wtexture & dispersion & single-time-Enh
2330 T1wmorphology & T1wtexture & dispersion
722 T1wdynamic & T1wmorphology & single-time-Enh & T2w
# print(FA[FA$allTestinfo.lesion_id==241,])
imgFA <- readPNG(paste0("Z:/Cristina/Section2/papernew_notes/images/", as.character(lesion_id),
"_", infoidx$cad_pt_no_txt, "_", infoidx$exam_a_number_txt, "_", infoidx$lesion_label, "_",
lesioninfo[lesioninfo$lesion_id == lesion_id, "find_t2_signal_int"], ".png"))
grid.raster(imgFA)
## with LMSIR
if (length(idLMSIR) > 0) {
for (i in 1:length(idLMSIR)) {
idx = idLMSIR[i]
lesion_id = FA[idx, ]$allTestinfo.lesion_id
print(lesion_id)
}
}
idx = c(1:nrow(FA))[c(FA$allTestinfo.lesion_id == lesion_id)]
infoidx = allTestinfo[allTestinfo$lesion_id == lesion_id, -c(20)]
print(infoidx)
lesion_id lesionfile cad_pt_no_txt anony_dob_datetime exam_img_dicom_txt
436 436 436_3046_7289130.vtk 3046 1970-11-16 00:00:00.000000 29427
exam_a_number_txt exam_dt_datetime exam_mri_cad_status_txt
436 7289130 2012-12-22 00:00:00.000000 Benign by pathology
cad_latest_mutation_status_int exam_find_mri_mass_yn exam_find_mri_nonmass_yn
436 None 1 0
exam_find_side_int proc_pt_procedure_id proc_proc_dt_datetime proc_proc_side_int
436 Right 2691 2013-01-22 00:00:00.000000 Right
proc_proc_source_int proc_proc_guid_int proc_proc_tp_int proc_lesion_comments_txt
436 Radiology US Core Needle Biopsy None
find_curve_int find_mri_dce_init_enh_int find_mri_dce_delay_enh_int BIRADS lesion_label
436 None N/A N/A 4 massB
lesion_diagnosis
436 FIBROADENOMA
print(mypresentRules(eachFATopRules[[idx]], colnames(X), fnames))
len freq err
6093 6 0.031 0
12940 4 0.049 0
519 2 0.176 0.053
1581 3 0.096 0.0570000000000001
459 2 0.064 0.0570000000000001
1541 2 0.162 0.0570000000000001
1996 2 0.184 0.069
331 3 0.106 0.07
442 3 0.237 0.07
3987 5 0.078 0.071
411 2 0.228 0.072
766 2 0.2 0.073
515 4 0.195 0.074
1338 2 0.193 0.077
183 2 0.232 0.079
336 2 0.246 0.081
11043 3 0.111 0.082
1128 2 0.215 0.085
1538 4 0.085 0.087
2330 3 0.216 0.093
722 4 0.136 0.095
condition
6093 SER(in) low to medium & Variance of spatial Margin Gradient low to very high & std 3D Sharpness of lesion margin low to medium & Inverse difference moment ptime4 medium to high & 2nd post-SE s12 very low & 2nd post-SE s17 low to medium
12940 Uptake(in) curve amplitude medium to high & SER(in) low to medium & Variance ptime3 low to medium & dispersion s11 very low
519 irregularity low & Energy ptime4 low to medium
1581 Difference variance ptime1 low & dispersion s16 low to medium & T2w margin gradient low
459 irregularity very low & dispersion s9 medium to high
1541 irregularity low & Energy ptime4 low to medium
1996 irregularity low & Energy ptime4 low to medium
331 SER(in) medium to high & irregularity low & Energy ptime4 low to medium
442 irregularity low & Variance ptime2 low to medium & Energy ptime4 very low to high
3987 Inverse difference moment ptime1 very low to high & dispersion s5 low to very high & dispersion s7 low to very high & 1st post-SE s19 low to very high & 3rd post-SE s12 very low
411 SER(in) low to medium & irregularity low
766 irregularity low & Energy ptime4 low to medium
515 SER(in) low & max Radial gradient medium to high & Sum variance ptime2 very low to high & 1st post-SE s10 low to very high
1338 irregularity low & Energy ptime4 low to medium
183 irregularity low & Inverse difference moment ptime4 low to medium
336 SER(in) low to medium & irregularity low
11043 Sum Entropy ptime1 low to medium & 1st post-SE s8 low to medium & last post-SE s17 high
1128 irregularity low & Energy ptime4 low to medium
1538 Uptake(in) curve amplitude medium to high & Sum Entropy ptime4 low to medium & dispersion s17 low to very high & 3rd post-SE s4 low
2330 irregularity low & Energy ptime3 low to medium & dispersion s5 low to very high
722 uptake average high & irregularity low to medium & 1st post-SE s8 low to medium & T2w radial gradient variance low
pred prob sumtempProb
6093 NC 0.6855391, 0.5934397, 0.5476637, 0.4856720, 0.6810844, 0.5714698 0.5941448
12940 NC 0.4874018, 0.5424656, 0.3437655, 0.4102728 0.4459764
519 NC 0.4703946, 0.2461935 0.358294
1581 NC 0.5724939, 0.3448565, 0.4659352 0.4610952
459 NC 0.6755135, 0.4776196 0.5765665
1541 NC 0.4792871, 0.2735542 0.3764207
1996 NC 0.5007048, 0.3009807 0.4008427
331 NC 0.4648444, 0.5897234, 0.3071130 0.4538936
442 NC 0.4378788, 0.2352466, 0.2721108 0.3150787
3987 NC 0.5232709, 0.5661026, 0.5040197, 0.5410826, 0.4760760 0.5221104
411 NC 0.4405761, 0.3043518 0.372464
766 NC 0.4867494, 0.2974405 0.392095
515 NC 0.2902278, 0.4509106, 0.3336921, 0.3700841 0.3612286
1338 NC 0.4991863, 0.2996197 0.399403
183 NC 0.4863329, 0.2652150 0.3757739
336 NC 0.5053493, 0.3706932 0.4380213
11043 NC 0.4335317, 0.4984163, 0.3944782 0.4421421
1128 NC 0.4553747, 0.2413562 0.3483655
1538 NC 0.6057217, 0.5218727, 0.4647596, 0.4578509 0.5125512
2330 NC 0.4678680, 0.2644552, 0.4902931 0.4075388
722 NC 0.4364043, 0.5007630, 0.5571853, 0.4727589 0.4917779
Ruletype
6093 T1wdynamic & T1wmorphology & T1wtexture & single-time-Enh
12940 T1wdynamic & T1wtexture & dispersion
519 T1wmorphology & T1wtexture
1581 T1wtexture & dispersion & T2w
459 T1wmorphology & dispersion
1541 T1wmorphology & T1wtexture
1996 T1wmorphology & T1wtexture
331 T1wdynamic & T1wmorphology & T1wtexture
442 T1wmorphology & T1wtexture
3987 T1wtexture & dispersion & single-time-Enh
411 T1wdynamic & T1wmorphology
766 T1wmorphology & T1wtexture
515 T1wdynamic & T1wmorphology & T1wtexture & single-time-Enh
1338 T1wmorphology & T1wtexture
183 T1wmorphology & T1wtexture
336 T1wdynamic & T1wmorphology
11043 T1wtexture & single-time-Enh
1128 T1wmorphology & T1wtexture
1538 T1wdynamic & T1wtexture & dispersion & single-time-Enh
2330 T1wmorphology & T1wtexture & dispersion
722 T1wdynamic & T1wmorphology & single-time-Enh & T2w
4) Present rules collect top for FIBROCYSTIC FI
eachFITopRules = list()
allFItoprules = c()
for (idx in 1:nrow(FI)) {
############## first analysis
X = FI[idx, 2:ncol(imgT2pLMSIRtest)]
y = FI[idx, "lesion_label"]
rulesoutputFI = mynewapplyLearnerxrules(topRulesFI, X, y, minerr = 0.1, minfrq = 10/627, classes,
gbmModel)
topRulesFI = rulesoutputFI[[1]]
if (length(rulesoutputFI) > 1) {
eachFITopRules[[idx]] = rulesoutputFI[[2]]
allFItoprules = rbind(allFItoprules, rulesoutputFI[[3]])
} else {
eachFITopRules[[idx]] = list()
allFItoprules = rbind(allFItoprules, 1:nrow(topRulesFI) * 0)
}
}
[1] "test complies with # rules: 5 out of 50"
[1] "test complies with # rules: 12 out of 50"
[1] "test complies with # rules: 13 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 6 out of 50"
[1] "test complies with # rules: 1 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 9 out of 50"
[1] "test complies with # rules: 17 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 6 out of 50"
[1] "test complies with # rules: 7 out of 50"
[1] "test complies with # rules: 16 out of 50"
[1] "test complies with # rules: 19 out of 50"
[1] "test complies with # rules: 19 out of 50"
[1] "test complies with # rules: 14 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 14 out of 50"
[1] "test complies with # rules: 13 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 20 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 5 out of 50"
[1] "test complies with # rules: 2 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 17 out of 50"
[1] "test complies with # rules: 12 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 11 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 11 out of 50"
[1] "test complies with # rules: 1 out of 50"
[1] "test complies with # rules: 11 out of 50"
[1] "test complies with # rules: 15 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 7 out of 50"
[1] "test complies with # rules: 10 out of 50"
[1] "test complies with # rules: 14 out of 50"
[1] "test complies with # rules: 14 out of 50"
[1] "test complies with # rules: 5 out of 50"
[1] "test complies with # rules: 5 out of 50"
[1] "test complies with # rules: 11 out of 50"
[1] "test complies with # rules: 11 out of 50"
[1] "test complies with # rules: 11 out of 50"
[1] "test complies with # rules: 8 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 4 out of 50"
[1] "test complies with # rules: 13 out of 50"
[1] "test complies with # rules: 14 out of 50"
[1] "test complies with # rules: 9 out of 50"
[1] "test complies with # rules: 12 out of 50"
[1] "test complies with # rules: 1 out of 50"
[1] "test complies with # rules: 7 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 9 out of 50"
[1] "test complies with # rules: 12 out of 50"
[1] "test complies with # rules: 6 out of 50"
[1] "test complies with # rules: 11 out of 50"
[1] "test complies with # rules: 1 out of 50"
[1] "test complies with # rules: 7 out of 50"
[1] "test complies with # rules: 3 out of 50"
[1] "test complies with # rules: 5 out of 50"
[1] "test complies with # rules: 7 out of 50"
[1] "test complies with # rules: 7 out of 50"
# take the occurance of each explaining rule (columns) per case(row) + lesion identifies
df = data.frame(cbind(allFItoprules, as.character(FI$allTestinfo.lesion_id), as.character(FI$allTestinfo.lesion_label),
as.character(FI$allTestinfo.lesion_diagnosis)), stringsAsFactors = FALSE)
colnames(df) <- c(as.character(1:nrow(topRulesFI)), "lesion_id", "lesion_label", "lesion_diagnosis")
cols = 1:nrow(topRulesFI)
df[, cols] = apply(df[, cols], 2, function(x) as.numeric(x))
cat(paste0("\n============== Top five explaining rules for FIBROCYSTIC (FI): n = ", nrow(FA), "\n"))
============== Top five explaining rules for FIBROCYSTIC (FI): n = 69
topFI = sort(colSums(df[, 1:nrow(topRulesFI)]), decreasing = TRUE)
print(topFI[1:5])
42 35 39 38 40
27 25 25 24 24
freqtopFI = topFI[1:5]
print(freqtopFI/nrow(FI))
42 35 39 38 40
0.3857143 0.3571429 0.3571429 0.3428571 0.3428571
rulesTopFI = as.numeric(names(topFI))
preserulesTopFI = mypresentRules(topRulesFI[rulesTopFI, ], colnames(X), fnames)
rownames(preserulesTopFI) <- NULL
print(preserulesTopFI)
len freq err
1 2 0.25 0.094
2 5 0.17 0.087
3 4 0.202 0.092
4 3 0.185 0.09
5 2 0.215 0.093
6 4 0.195 0.074
7 2 0.193 0.077
8 2 0.197 0.073
9 2 0.184 0.069
10 2 0.162 0.0570000000000001
11 5 0.168 0.075
12 3 0.127 0.043
13 3 0.177 0.093
14 4 0.094 0.077
15 2 0.124 0.088
16 2 0.091 0.082
17 4 0.136 0.095
18 3 0.053 0.034
19 4 0.103 0.088
20 4 0.066 0.028
21 6 0.096 0.0580000000000001
22 3 0.06 0.0610000000000001
23 2 0.052 0.071
24 3 0.095 0.096
25 3 0.116 0.095
26 4 0.041 0
27 6 0.047 0.038
28 5 0.07 0.077
29 3 0.108 0.083
30 2 0.057 0.097
31 4 0.057 0.097
32 2 0.071 0.051
33 3 0.076 0.095
34 4 0.057 0.032
35 4 0.055 0.033
36 3 0.048 0.038
37 2 0.048 0.038
38 5 0.038 0.048
39 3 0.057 0.0649999999999999
40 3 0.057 0.097
41 4 0.031 0.0590000000000001
42 2 0.045 0.08
43 4 0.066 0.083
44 2 0.044 0.042
45 3 0.038 0.095
46 3 0.031 0
47 2 0.135 0.0679999999999999
48 3 0.107 0.0679999999999999
49 3 0.08 0.0679999999999999
50 2 0.14 0.078
condition
1 irregularity low & Inverse difference moment ptime4 low to medium
2 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
3 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
4 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
5 SER(in) low & T2w Energy medium to high
6 SER(in) low & max Radial gradient medium to high & Sum variance ptime2 very low to high & 1st post-SE s10 low to very high
7 irregularity low & Energy ptime4 low to medium
8 irregularity low & Energy ptime4 low to medium
9 irregularity low & Energy ptime4 low to medium
10 irregularity low & Energy ptime4 low to medium
11 Initial Uptake slope(in) low & uptake average low to very high & 1st post-SE s10 low to very high & T2w std SI low to medium & T2w margin gradient variance very low to high
12 uptake skewness low & irregularity very low & dispersion s1 low to very high
13 SER(rim) low & Difference variance ptime1 low & T2w Correlation low to very high
14 Initial Uptake slope(in) low to medium & Curvature at Time-to-peak(in) low to very high & dispersion s10 low to very high & 2nd post-SE s11 high
15 circularity high & T2w radial gradient variance medium to high
16 circularity high & Sum average ptime1 low
17 uptake average high & irregularity low to medium & 1st post-SE s8 low to medium & T2w radial gradient variance low
18 enhancement-variance at first time-point(in) very low & irregularity very low & max T2w SI low to very high
19 SER(rim) very low to high & dispersion s1 very low & dispersion s14 low & 2nd post-SE s16 high
20 enhancement-variance increasing rate(rim) low to medium & Max Margin Gradient low & Entropy ptime1 low & Sum average ptime2 very low to high
21 Area Under Uptake curve(in) very low to high & Variance ptime1 very low & Energy ptime4 very low to high & dispersion s16 low to very high & 2nd post-SE s17 low to very high & 3rd post-SE s6 low to very high
22 circularity high & T2w radial gradient variance medium to high & T2w radial gradient variance very low to high
23 SER(in) low & enhancement-variance increasing rate(in) very low
24 enhancement-variance decreasing rate(rim) high & Sum variance ptime2 low to medium & last post-SE s10 medium to high
25 SER(in) very low & enhancement-variance increasing rate(in) very low to high & enhancement-variance decreasing rate(rim) very low to high
26 Initial Uptake slope(in) low & uptake average high & 1st post-SE s15 low to very high & 1st post-SE s16 low to very high
27 circularity high & dispersion s5 low to very high & dispersion s10 low to very high & 3rd post-SE s7 very low to high & 3rd post-SE s12 medium to high & last post-SE s17 low
28 SER(rim) very low to high & dispersion s14 very low & dispersion s15 very low to high & 1st post-SE s4 low to very high & T2w Entropy low
29 irregularity low to medium & 3rd post-SE s10 low to very high & 3rd post-SE s16 low
30 max relative signal enhancement(rim) medium to high & change in Variance of spatial Margin Gradient very high
31 enhancement-variance at first time-point(rim) low to medium & uptake variance medium to high & max Radial gradient low & dispersion s2 medium to high
32 3rd post-SE s10 low to very high & last post-SE s11 very low
33 enhancement-variance increasing rate(rim) low to medium & dispersion s16 very low & last post-SE s8 high
34 Max Radial gradient variance very low & Sum average ptime1 medium to high & 1st post-SE s16 low to very high & T2w Inverse difference moment low to very high
35 min uptake very low to high & mean 3D Sharpness of lesion margin very low & Energy ptime4 low to medium & dispersion s16 low
36 SER(in) low & irregularity medium to high & last post-SE s2 very low
37 Energy ptime1 very low to high & Entropy ptime2 very low
38 Max Radial gradient variance very low & Sum average ptime3 medium to high & Entropy ptime4 very low to high & dispersion s18 low & 2nd post-SE s15 very low to high
39 irregularity very low & Difference variance ptime3 very low to high & T2w radial gradient variance medium to high
40 SER(rim) low to medium & irregularity medium to high & last post-SE s2 very low
41 Rate of signal increase(in) low & Rate of signal increase(in) medium to high & 1st post-SE s15 low to very high & last post-SE s8 low to very high
42 dispersion s5 very low & 1st post-SE s11 low
43 uptake skewness medium to high & irregularity medium to high & kurtosis T2w SI low to very high & T2w average radial gradient very low
44 irregularity very low & T2w radial gradient variance medium to high
45 Rate of signal increase(rim) very low & dispersion s17 low to very high & T2w mean SI low to very high
46 SER(rim) very low & 1st post-SE s6 very low & last post-SE s7 very low
47 irregularity high & Sum variance ptime1 high
48 irregularity medium to high & Max Radial gradient variance medium to high & Variance ptime1 very high
49 uptake average high & Inverse difference moment ptime2 low to medium & 1st post-SE s8 high
50 irregularity high & Sum variance ptime1 high
pred prob sumtempProb
1 NC 0.4236079, 0.2408969 0.3322524
2 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
3 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
4 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
5 NC 0.4881946, 0.2745578 0.3813762
6 NC 0.2902278, 0.4509106, 0.3336921, 0.3700841 0.3612286
7 NC 0.4991863, 0.2996197 0.399403
8 NC 0.4694149, 0.2405692 0.3549921
9 NC 0.5007048, 0.3009807 0.4008427
10 NC 0.4792871, 0.2735542 0.3764207
11 NC 0.4508790, 0.4713496, 0.5509649, 0.5310208, 0.5073532 0.5023135
12 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
13 NC 0.5505793, 0.3818076, 0.5017071 0.4780313
14 NC 0.4452511, 0.5362599, 0.3412410, 0.4844197 0.4517929
15 NC 0.5514954, 0.4847561 0.5181258
16 NC 0.5779883, 0.4539037 0.515946
17 NC 0.4364043, 0.5007630, 0.5571853, 0.4727589 0.4917779
18 NC 0.4848342, 0.5546800, 0.6219773 0.5538305
19 NC 0.4581848, 0.5217262, 0.6139028, 0.5050821 0.524724
20 NC 0.4810853, 0.2872408, 0.4052440, 0.3282516 0.3754554
21 NC 0.4755872, 0.5433402, 0.4788114, 0.4381729, 0.4557238, 0.5067061 0.4830569
22 NC 0.6781025, 0.4757408, 0.5921319 0.5819917
23 NC 0.6114913, 0.4662233 0.5388573
24 NC 0.4806604, 0.4285987, 0.5949174 0.5013922
25 NC 0.5192031, 0.5443866, 0.4975629 0.5203842
26 NC 0.6920559, 0.4833696, 0.7240647, 0.5912338 0.622681
27 NC 0.6372325, 0.7199635, 0.4684946, 0.4917864, 0.5568750, 0.4652017 0.5565923
28 NC 0.4499065, 0.4352475, 0.4759258, 0.4943733, 0.5792785 0.4869463
29 NC 0.5052503, 0.4047316, 0.3668232 0.4256017
30 NC 0.6236805, 0.4747261 0.5492033
31 NC 0.5904771, 0.6088937, 0.5063315, 0.6877946 0.5983742
32 NC 0.5144900, 0.4830707 0.4987804
33 NC 0.3132262, 0.5008952, 0.5531483 0.4557566
34 NC 0.6231637, 0.2928371, 0.5364463, 0.5693335 0.5054452
35 NC 0.4686661, 0.3111970, 0.4932763, 0.4507027 0.4309605
36 NC 0.6131108, 0.4701726, 0.3805070 0.4879301
37 NC 0.5127610, 0.4835754 0.4981682
38 NC 0.4289456, 0.6226296, 0.5110246, 0.5385531, 0.4767274 0.5155761
39 NC 0.5914519, 0.4717202, 0.4894149 0.517529
40 NC 0.5743398, 0.4464800, 0.3780448 0.4662882
41 NC 0.5271721, 0.3903370, 0.5439983, 0.4908403 0.488087
42 NC 0.4735013, 0.6948949 0.5841981
43 NC 0.6209921, 0.4870514, 0.5075204, 0.4635613 0.5197813
44 NC 0.5748740, 0.4661645 0.5205192
45 NC 0.5582364, 0.5165599, 0.5742535 0.5496832
46 NC 0.6420296, 0.5124139, 0.4394809 0.5313081
47 C 0.5087730, 0.8044078 0.6565904
48 C 0.4969203, 0.6008289, 0.5469925 0.5482472
49 C 0.5436611, 0.6397459, 0.5003391 0.5612487
50 C 0.4957177, 0.7767643 0.636241
Ruletype
1 T1wmorphology & T1wtexture
2 T1wmorphology & T1wtexture & dispersion & T2w
3 T1wmorphology & dispersion & T2w
4 T1wdynamic & T1wmorphology
5 T1wdynamic & T2w
6 T1wdynamic & T1wmorphology & T1wtexture & single-time-Enh
7 T1wmorphology & T1wtexture
8 T1wmorphology & T1wtexture
9 T1wmorphology & T1wtexture
10 T1wmorphology & T1wtexture
11 T1wdynamic & single-time-Enh & T2w
12 T1wdynamic & T1wmorphology & dispersion
13 T1wdynamic & T1wtexture & T2w
14 T1wdynamic & dispersion & single-time-Enh
15 T1wmorphology & T2w
16 T1wmorphology & T1wtexture
17 T1wdynamic & T1wmorphology & single-time-Enh & T2w
18 T1wdynamic & T1wmorphology & T2w
19 T1wdynamic & dispersion & single-time-Enh
20 T1wdynamic & T1wmorphology & T1wtexture
21 T1wdynamic & T1wtexture & dispersion & single-time-Enh
22 T1wmorphology & T2w
23 T1wdynamic
24 T1wdynamic & T1wtexture & single-time-Enh
25 T1wdynamic
26 T1wdynamic & single-time-Enh
27 T1wmorphology & dispersion & single-time-Enh
28 T1wdynamic & dispersion & single-time-Enh & T2w
29 T1wmorphology & single-time-Enh
30 T1wdynamic & T1wmorphology
31 T1wdynamic & T1wmorphology & dispersion
32 single-time-Enh
33 T1wdynamic & dispersion & single-time-Enh
34 T1wmorphology & T1wtexture & single-time-Enh & T2w
35 T1wdynamic & T1wmorphology & T1wtexture & dispersion
36 T1wdynamic & T1wmorphology & single-time-Enh
37 T1wtexture
38 T1wmorphology & T1wtexture & dispersion & single-time-Enh
39 T1wmorphology & T1wtexture & T2w
40 T1wdynamic & T1wmorphology & single-time-Enh
41 T1wdynamic & single-time-Enh
42 dispersion & single-time-Enh
43 T1wdynamic & T1wmorphology & T2w
44 T1wmorphology & T2w
45 T1wdynamic & dispersion & T2w
46 T1wdynamic & single-time-Enh
47 T1wmorphology & T1wtexture
48 T1wmorphology & T1wtexture
49 T1wdynamic & T1wtexture & single-time-Enh
50 T1wmorphology & T1wtexture
# display a case that meets them all
casesFI = df[, c(rulesTopFI, nrow(topRulesFI) + 1, nrow(topRulesFI) + 2, nrow(topRulesFI) + 3)]
print("Sorted cases meeting top five explaining rules for FIBROCYSTIC (FI):")
[1] "Sorted cases meeting top five explaining rules for FIBROCYSTIC (FI):"
topcasesFI = casesFI[sort(rowSums(casesFI[, 1:5]), index = TRUE, decreasing = TRUE)$ix, ]
print(topcasesFI)
42 35 39 38 40 25 27 24 22 14 26 11 41 29 37 32 46 6 36 3 15 17 23 47 45 1 8 28 33 49 50 13
9 1 1 1 1 1 0 1 1 1 1 0 1 0 0 1 0 1 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0
14 1 1 1 1 1 1 1 1 1 1 0 1 1 0 1 1 0 0 0 1 1 1 0 1 0 0 0 0 0 1 0 0
15 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 0 0 0 1 1 1 0 0 0 0 0 0 0 1 0 0
21 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 1 0 0 1 0 0 1 0 0 1 0 0 0
3 1 1 1 1 0 0 1 1 1 1 0 0 0 0 1 1 0 0 0 0 1 1 0 0 0 0 0 0 0 1 0 0
8 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0
13 1 1 1 1 0 0 1 1 1 1 0 1 1 0 1 1 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0
18 1 1 0 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 1 0 0 0 1 0 1 0 0 1 0 1 0 0
26 1 1 1 0 1 1 1 1 1 1 1 0 0 1 0 0 1 0 1 0 0 0 1 0 0 1 0 0 0 0 0 0
50 1 0 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
54 1 0 1 1 1 1 1 1 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
55 1 1 1 1 0 0 1 1 1 1 0 1 0 1 0 1 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0
5 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
16 1 1 1 0 0 0 1 1 1 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 1 0 1 0 0 0
19 1 0 1 0 1 1 1 1 1 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 1 0 0 0 1 0 0 0
28 1 1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0
30 1 1 1 0 0 0 1 1 1 1 0 0 0 0 1 1 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0
32 1 0 1 1 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
33 1 0 1 1 0 0 1 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
44 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 1 0 1 0 0 1 0 0 0 0 1 0 0
45 1 0 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 1 1 1 0 0 1 0 0 1 0 0 0 0 0 0
57 1 1 1 0 0 0 1 1 1 1 0 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1
64 1 1 1 0 0 0 1 1 1 1 0 0 0 1 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0
2 0 1 1 0 0 0 1 1 1 0 0 1 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0
12 0 1 1 0 0 0 0 0 0 0 1 0 1 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
35 1 1 0 0 0 0 1 1 1 1 0 0 0 0 1 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1
36 0 0 0 1 1 1 0 0 0 0 1 1 1 0 1 0 0 1 0 0 0 1 1 0 0 1 0 0 0 0 0 0
42 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0
43 1 0 0 1 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
48 0 1 0 1 0 0 0 0 0 0 1 1 1 1 0 0 0 1 0 1 1 0 0 0 0 0 1 0 0 0 0 0
51 0 0 1 1 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0
56 1 1 0 0 0 0 1 1 1 1 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
62 1 0 0 0 1 1 0 0 0 0 1 0 1 1 0 0 0 0 0 0 1 0 1 0 1 1 1 0 0 0 0 0
63 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0
68 0 1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1
4 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
11 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0
17 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
20 0 0 0 0 1 1 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
23 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0
27 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 0 0 0 0 0 0 1 1 0 0 1
37 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
39 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0
46 0 0 0 0 1 1 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
47 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
49 0 0 0 0 1 1 0 0 0 0 1 0 1 0 0 0 0 0 1 0 1 0 0 0 1 0 0 1 1 0 0 0
52 0 0 0 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
61 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 1 1
66 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0
69 0 0 0 0 1 1 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0
70 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
7 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
10 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
22 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0
24 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
25 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
31 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
34 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
38 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
41 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
53 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0
58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
59 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0
60 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
43 4 5 7 9 12 18 48 16 31 34 10 44 2 19 20 21 30 lesion_id lesion_label lesion_diagnosis
9 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 74 massB FIBROCYSTIC
14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 411 nonmassB FIBROCYSTIC
15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 412 nonmassB FIBROCYSTIC
21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 311 massB FIBROCYSTIC
3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 301 nonmassB FIBROCYSTIC
8 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 66 nonmassB FIBROCYSTIC
13 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 383 nonmassB FIBROCYSTIC
18 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 212 massB FIBROCYSTIC
26 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 135 massB FIBROCYSTIC
50 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 627 massB FIBROCYSTIC
54 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 48 massB FIBROCYSTIC
55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 263 massB FIBROCYSTIC
5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 503 massB FIBROCYSTIC
16 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 93 massB FIBROCYSTIC
19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 213 massB FIBROCYSTIC
28 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 317 nonmassB FIBROCYSTIC
30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 396 nonmassB FIBROCYSTIC
32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 613 nonmassB FIBROCYSTIC
33 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 10 massB FIBROCYSTIC
44 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 0 166 massB FIBROCYSTIC
45 0 1 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 193 nonmassB FIBROCYSTIC
57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 267 nonmassB FIBROCYSTIC
64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 massB FIBROCYSTIC
2 0 0 1 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 228 massB FIBROCYSTIC
12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 288 massB FIBROCYSTIC
35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 256 massB FIBROCYSTIC
36 0 0 0 0 1 0 1 0 0 1 0 1 0 0 0 0 0 0 274 massB FIBROCYSTIC
42 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 79 nonmassB FIBROCYSTIC
43 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 137 massB FIBROCYSTIC
48 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 579 nonmassB FIBROCYSTIC
51 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 26 massB FIBROCYSTIC
56 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 266 nonmassB FIBROCYSTIC
62 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 590 nonmassB FIBROCYSTIC
63 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 massB FIBROCYSTIC
68 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 330 nonmassB FIBROCYSTIC
4 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 0 1 415 nonmassB FIBROCYSTIC
11 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 287 massB FIBROCYSTIC
17 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 146 nonmassB FIBROCYSTIC
20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 233 massB FIBROCYSTIC
23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 419 nonmassB FIBROCYSTIC
27 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 302 massB FIBROCYSTIC
37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 636 nonmassB FIBROCYSTIC
39 0 1 0 0 0 0 1 0 0 1 0 1 1 0 0 0 0 0 76 massB FIBROCYSTIC
46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 348 nonmassB FIBROCYSTIC
47 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 356 nonmassB FIBROCYSTIC
49 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 211 massB FIBROCYSTIC
52 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 nonmassB FIBROCYSTIC
61 0 0 0 1 0 0 0 1 0 0 1 0 0 1 0 0 0 0 537 nonmassB FIBROCYSTIC
66 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 141 massB FIBROCYSTIC
69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 468 massB FIBROCYSTIC
70 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 469 nonmassB FIBROCYSTIC
1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 1 165 massB FIBROCYSTIC
6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 nonmassB FIBROCYSTIC
7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 nonmassB FIBROCYSTIC
10 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 123 massB FIBROCYSTIC
22 0 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 0 339 nonmassB FIBROCYSTIC
24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 461 nonmassB FIBROCYSTIC
25 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 462 massB FIBROCYSTIC
29 0 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 0 338 nonmassB FIBROCYSTIC
31 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 558 massB FIBROCYSTIC
34 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 255 massB FIBROCYSTIC
38 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 75 massB FIBROCYSTIC
40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 236 nonmassB FIBROCYSTIC
41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 524 massB FIBROCYSTIC
53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 massB FIBROCYSTIC
58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 307 massB FIBROCYSTIC
59 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 426 massB FIBROCYSTIC
60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 432 massB FIBROCYSTIC
65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 56 nonmassB FIBROCYSTIC
67 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 231 nonmassB FIBROCYSTIC
print("Fine explaining rules for FIBROCYSTIC (FI) with LMSIR:")
[1] "Fine explaining rules for FIBROCYSTIC (FI) with LMSIR:"
LMSIRfeatureflag = c()
idLMSIR = c()
for (i in 1:length(eachFITopRules)) {
if (length(eachFITopRules[[i]]) > 0) {
rules = mypresentRules(eachFITopRules[[i]], colnames(X), fnames)
LMSIRwtop5 = "LMSIR" %in% unlist(strsplit(unlist(strsplit(rules$condition, split = " & ")),
split = " "))
if (LMSIRwtop5) {
LMSIRfeatureflag = c(LMSIRfeatureflag, LMSIRwtop5)
print(i)
print(rules)
idLMSIR = c(idLMSIR, i)
} else {
LMSIRfeatureflag = c(LMSIRfeatureflag, FALSE)
}
} else {
LMSIRfeatureflag = c(LMSIRfeatureflag, FALSE)
}
}
[1] 2
len freq err
4971 4 0.055 0.033
7103 2 0.044 0.042
12721 3 0.127 0.043
1073 3 0.06 0.0610000000000001
1578 3 0.057 0.0649999999999999
1996 2 0.184 0.069
883 2 0.197 0.073
1338 2 0.193 0.077
5547 5 0.17 0.087
3902 2 0.124 0.088
6375 4 0.202 0.092
4809 3 0.095 0.096
condition
4971 min uptake very low to high & mean 3D Sharpness of lesion margin very low & Energy ptime4 low to medium & dispersion s16 low
7103 irregularity very low & T2w radial gradient variance medium to high
12721 uptake skewness low & irregularity very low & dispersion s1 low to very high
1073 circularity high & T2w radial gradient variance medium to high & T2w radial gradient variance very low to high
1578 irregularity very low & Difference variance ptime3 very low to high & T2w radial gradient variance medium to high
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
1338 irregularity low & Energy ptime4 low to medium
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
3902 circularity high & T2w radial gradient variance medium to high
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
4809 enhancement-variance decreasing rate(rim) high & Sum variance ptime2 low to medium & last post-SE s10 medium to high
pred prob sumtempProb
4971 NC 0.4686661, 0.3111970, 0.4932763, 0.4507027 0.4309605
7103 NC 0.5748740, 0.4661645 0.5205192
12721 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
1073 NC 0.6781025, 0.4757408, 0.5921319 0.5819917
1578 NC 0.5914519, 0.4717202, 0.4894149 0.517529
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
1338 NC 0.4991863, 0.2996197 0.399403
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
3902 NC 0.5514954, 0.4847561 0.5181258
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
4809 NC 0.4806604, 0.4285987, 0.5949174 0.5013922
Ruletype
4971 T1wdynamic & T1wmorphology & T1wtexture & dispersion
7103 T1wmorphology & T2w
12721 T1wdynamic & T1wmorphology & dispersion
1073 T1wmorphology & T2w
1578 T1wmorphology & T1wtexture & T2w
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
1338 T1wmorphology & T1wtexture
5547 T1wmorphology & T1wtexture & dispersion & T2w
3902 T1wmorphology & T2w
6375 T1wmorphology & dispersion & T2w
4809 T1wdynamic & T1wtexture & single-time-Enh
[1] 3
len freq err
1541 2 0.162 0.0570000000000001
12632 6 0.096 0.0580000000000001
1073 3 0.06 0.0610000000000001
1996 2 0.184 0.069
883 2 0.197 0.073
1338 2 0.193 0.077
7750 2 0.091 0.082
5547 5 0.17 0.087
3902 2 0.124 0.088
8424 3 0.185 0.09
6375 4 0.202 0.092
750 2 0.25 0.094
9527 2 0.057 0.097
condition
1541 irregularity low & Energy ptime4 low to medium
12632 Area Under Uptake curve(in) very low to high & Variance ptime1 very low & Energy ptime4 very low to high & dispersion s16 low to very high & 2nd post-SE s17 low to very high & 3rd post-SE s6 low to very high
1073 circularity high & T2w radial gradient variance medium to high & T2w radial gradient variance very low to high
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
1338 irregularity low & Energy ptime4 low to medium
7750 circularity high & Sum average ptime1 low
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
3902 circularity high & T2w radial gradient variance medium to high
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
9527 max relative signal enhancement(rim) medium to high & change in Variance of spatial Margin Gradient very high
pred prob sumtempProb
1541 NC 0.4792871, 0.2735542 0.3764207
12632 NC 0.4755872, 0.5433402, 0.4788114, 0.4381729, 0.4557238, 0.5067061 0.4830569
1073 NC 0.6781025, 0.4757408, 0.5921319 0.5819917
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
1338 NC 0.4991863, 0.2996197 0.399403
7750 NC 0.5779883, 0.4539037 0.515946
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
3902 NC 0.5514954, 0.4847561 0.5181258
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
750 NC 0.4236079, 0.2408969 0.3322524
9527 NC 0.6236805, 0.4747261 0.5492033
Ruletype
1541 T1wmorphology & T1wtexture
12632 T1wdynamic & T1wtexture & dispersion & single-time-Enh
1073 T1wmorphology & T2w
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
1338 T1wmorphology & T1wtexture
7750 T1wmorphology & T1wtexture
5547 T1wmorphology & T1wtexture & dispersion & T2w
3902 T1wmorphology & T2w
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
750 T1wmorphology & T1wtexture
9527 T1wdynamic & T1wmorphology
[1] 5
len freq err
1073 3 0.06 0.0610000000000001
7750 2 0.091 0.082
5547 5 0.17 0.087
3902 2 0.124 0.088
8424 3 0.185 0.09
6375 4 0.202 0.092
condition
1073 circularity high & T2w radial gradient variance medium to high & T2w radial gradient variance very low to high
7750 circularity high & Sum average ptime1 low
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
3902 circularity high & T2w radial gradient variance medium to high
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
pred prob sumtempProb
1073 NC 0.6781025, 0.4757408, 0.5921319 0.5819917
7750 NC 0.5779883, 0.4539037 0.515946
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
3902 NC 0.5514954, 0.4847561 0.5181258
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
Ruletype
1073 T1wmorphology & T2w
7750 T1wmorphology & T1wtexture
5547 T1wmorphology & T1wtexture & dispersion & T2w
3902 T1wmorphology & T2w
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
[1] 8
len freq err
1233 4 0.066 0.028
3314 5 0.07 0.077
7111 4 0.094 0.077
7750 2 0.091 0.082
5547 5 0.17 0.087
8424 3 0.185 0.09
6375 4 0.202 0.092
750 2 0.25 0.094
2209 3 0.076 0.095
condition
1233 enhancement-variance increasing rate(rim) low to medium & Max Margin Gradient low & Entropy ptime1 low & Sum average ptime2 very low to high
3314 SER(rim) very low to high & dispersion s14 very low & dispersion s15 very low to high & 1st post-SE s4 low to very high & T2w Entropy low
7111 Initial Uptake slope(in) low to medium & Curvature at Time-to-peak(in) low to very high & dispersion s10 low to very high & 2nd post-SE s11 high
7750 circularity high & Sum average ptime1 low
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
2209 enhancement-variance increasing rate(rim) low to medium & dispersion s16 very low & last post-SE s8 high
pred prob sumtempProb
1233 NC 0.4810853, 0.2872408, 0.4052440, 0.3282516 0.3754554
3314 NC 0.4499065, 0.4352475, 0.4759258, 0.4943733, 0.5792785 0.4869463
7111 NC 0.4452511, 0.5362599, 0.3412410, 0.4844197 0.4517929
7750 NC 0.5779883, 0.4539037 0.515946
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
750 NC 0.4236079, 0.2408969 0.3322524
2209 NC 0.3132262, 0.5008952, 0.5531483 0.4557566
Ruletype
1233 T1wdynamic & T1wmorphology & T1wtexture
3314 T1wdynamic & dispersion & single-time-Enh & T2w
7111 T1wdynamic & dispersion & single-time-Enh
7750 T1wmorphology & T1wtexture
5547 T1wmorphology & T1wtexture & dispersion & T2w
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
750 T1wmorphology & T1wtexture
2209 T1wdynamic & dispersion & single-time-Enh
[1] 9
len freq err
1342 3 0.053 0.034
12721 3 0.127 0.043
4833 5 0.038 0.048
1541 2 0.162 0.0570000000000001
1578 3 0.057 0.0649999999999999
1996 2 0.184 0.069
2076 2 0.052 0.071
883 2 0.197 0.073
1338 2 0.193 0.077
5547 5 0.17 0.087
3902 2 0.124 0.088
8424 3 0.185 0.09
6375 4 0.202 0.092
726 2 0.215 0.093
750 2 0.25 0.094
5386 3 0.116 0.095
722 4 0.136 0.095
condition
1342 enhancement-variance at first time-point(in) very low & irregularity very low & max T2w SI low to very high
12721 uptake skewness low & irregularity very low & dispersion s1 low to very high
4833 Max Radial gradient variance very low & Sum average ptime3 medium to high & Entropy ptime4 very low to high & dispersion s18 low & 2nd post-SE s15 very low to high
1541 irregularity low & Energy ptime4 low to medium
1578 irregularity very low & Difference variance ptime3 very low to high & T2w radial gradient variance medium to high
1996 irregularity low & Energy ptime4 low to medium
2076 SER(in) low & enhancement-variance increasing rate(in) very low
883 irregularity low & Energy ptime4 low to medium
1338 irregularity low & Energy ptime4 low to medium
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
3902 circularity high & T2w radial gradient variance medium to high
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
726 SER(in) low & T2w Energy medium to high
750 irregularity low & Inverse difference moment ptime4 low to medium
5386 SER(in) very low & enhancement-variance increasing rate(in) very low to high & enhancement-variance decreasing rate(rim) very low to high
722 uptake average high & irregularity low to medium & 1st post-SE s8 low to medium & T2w radial gradient variance low
pred prob sumtempProb
1342 NC 0.4848342, 0.5546800, 0.6219773 0.5538305
12721 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
4833 NC 0.4289456, 0.6226296, 0.5110246, 0.5385531, 0.4767274 0.5155761
1541 NC 0.4792871, 0.2735542 0.3764207
1578 NC 0.5914519, 0.4717202, 0.4894149 0.517529
1996 NC 0.5007048, 0.3009807 0.4008427
2076 NC 0.6114913, 0.4662233 0.5388573
883 NC 0.4694149, 0.2405692 0.3549921
1338 NC 0.4991863, 0.2996197 0.399403
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
3902 NC 0.5514954, 0.4847561 0.5181258
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
726 NC 0.4881946, 0.2745578 0.3813762
750 NC 0.4236079, 0.2408969 0.3322524
5386 NC 0.5192031, 0.5443866, 0.4975629 0.5203842
722 NC 0.4364043, 0.5007630, 0.5571853, 0.4727589 0.4917779
Ruletype
1342 T1wdynamic & T1wmorphology & T2w
12721 T1wdynamic & T1wmorphology & dispersion
4833 T1wmorphology & T1wtexture & dispersion & single-time-Enh
1541 T1wmorphology & T1wtexture
1578 T1wmorphology & T1wtexture & T2w
1996 T1wmorphology & T1wtexture
2076 T1wdynamic
883 T1wmorphology & T1wtexture
1338 T1wmorphology & T1wtexture
5547 T1wmorphology & T1wtexture & dispersion & T2w
3902 T1wmorphology & T2w
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
726 T1wdynamic & T2w
750 T1wmorphology & T1wtexture
5386 T1wdynamic
722 T1wdynamic & T1wmorphology & single-time-Enh & T2w
[1] 12
len freq err
1233 4 0.066 0.028
5316 5 0.168 0.075
7750 2 0.091 0.082
5547 5 0.17 0.087
6375 4 0.202 0.092
5658 3 0.177 0.093
722 4 0.136 0.095
condition
1233 enhancement-variance increasing rate(rim) low to medium & Max Margin Gradient low & Entropy ptime1 low & Sum average ptime2 very low to high
5316 Initial Uptake slope(in) low & uptake average low to very high & 1st post-SE s10 low to very high & T2w std SI low to medium & T2w margin gradient variance very low to high
7750 circularity high & Sum average ptime1 low
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
5658 SER(rim) low & Difference variance ptime1 low & T2w Correlation low to very high
722 uptake average high & irregularity low to medium & 1st post-SE s8 low to medium & T2w radial gradient variance low
pred prob sumtempProb
1233 NC 0.4810853, 0.2872408, 0.4052440, 0.3282516 0.3754554
5316 NC 0.4508790, 0.4713496, 0.5509649, 0.5310208, 0.5073532 0.5023135
7750 NC 0.5779883, 0.4539037 0.515946
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
5658 NC 0.5505793, 0.3818076, 0.5017071 0.4780313
722 NC 0.4364043, 0.5007630, 0.5571853, 0.4727589 0.4917779
Ruletype
1233 T1wdynamic & T1wmorphology & T1wtexture
5316 T1wdynamic & single-time-Enh & T2w
7750 T1wmorphology & T1wtexture
5547 T1wmorphology & T1wtexture & dispersion & T2w
6375 T1wmorphology & dispersion & T2w
5658 T1wdynamic & T1wtexture & T2w
722 T1wdynamic & T1wmorphology & single-time-Enh & T2w
[1] 13
len freq err
1233 4 0.066 0.028
1342 3 0.053 0.034
12721 3 0.127 0.043
1541 2 0.162 0.0570000000000001
12632 6 0.096 0.0580000000000001
1578 3 0.057 0.0649999999999999
1996 2 0.184 0.069
883 2 0.197 0.073
1338 2 0.193 0.077
7750 2 0.091 0.082
5547 5 0.17 0.087
3902 2 0.124 0.088
8424 3 0.185 0.09
6375 4 0.202 0.092
5658 3 0.177 0.093
750 2 0.25 0.094
condition
1233 enhancement-variance increasing rate(rim) low to medium & Max Margin Gradient low & Entropy ptime1 low & Sum average ptime2 very low to high
1342 enhancement-variance at first time-point(in) very low & irregularity very low & max T2w SI low to very high
12721 uptake skewness low & irregularity very low & dispersion s1 low to very high
1541 irregularity low & Energy ptime4 low to medium
12632 Area Under Uptake curve(in) very low to high & Variance ptime1 very low & Energy ptime4 very low to high & dispersion s16 low to very high & 2nd post-SE s17 low to very high & 3rd post-SE s6 low to very high
1578 irregularity very low & Difference variance ptime3 very low to high & T2w radial gradient variance medium to high
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
1338 irregularity low & Energy ptime4 low to medium
7750 circularity high & Sum average ptime1 low
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
3902 circularity high & T2w radial gradient variance medium to high
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
5658 SER(rim) low & Difference variance ptime1 low & T2w Correlation low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
pred prob sumtempProb
1233 NC 0.4810853, 0.2872408, 0.4052440, 0.3282516 0.3754554
1342 NC 0.4848342, 0.5546800, 0.6219773 0.5538305
12721 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
1541 NC 0.4792871, 0.2735542 0.3764207
12632 NC 0.4755872, 0.5433402, 0.4788114, 0.4381729, 0.4557238, 0.5067061 0.4830569
1578 NC 0.5914519, 0.4717202, 0.4894149 0.517529
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
1338 NC 0.4991863, 0.2996197 0.399403
7750 NC 0.5779883, 0.4539037 0.515946
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
3902 NC 0.5514954, 0.4847561 0.5181258
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
5658 NC 0.5505793, 0.3818076, 0.5017071 0.4780313
750 NC 0.4236079, 0.2408969 0.3322524
Ruletype
1233 T1wdynamic & T1wmorphology & T1wtexture
1342 T1wdynamic & T1wmorphology & T2w
12721 T1wdynamic & T1wmorphology & dispersion
1541 T1wmorphology & T1wtexture
12632 T1wdynamic & T1wtexture & dispersion & single-time-Enh
1578 T1wmorphology & T1wtexture & T2w
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
1338 T1wmorphology & T1wtexture
7750 T1wmorphology & T1wtexture
5547 T1wmorphology & T1wtexture & dispersion & T2w
3902 T1wmorphology & T2w
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
5658 T1wdynamic & T1wtexture & T2w
750 T1wmorphology & T1wtexture
[1] 14
len freq err
1233 4 0.066 0.028
12721 3 0.127 0.043
1541 2 0.162 0.0570000000000001
12632 6 0.096 0.0580000000000001
1073 3 0.06 0.0610000000000001
1996 2 0.184 0.069
883 2 0.197 0.073
515 4 0.195 0.074
1338 2 0.193 0.077
7750 2 0.091 0.082
5547 5 0.17 0.087
3902 2 0.124 0.088
8424 3 0.185 0.09
6375 4 0.202 0.092
726 2 0.215 0.093
5658 3 0.177 0.093
750 2 0.25 0.094
4809 3 0.095 0.096
9527 2 0.057 0.097
condition
1233 enhancement-variance increasing rate(rim) low to medium & Max Margin Gradient low & Entropy ptime1 low & Sum average ptime2 very low to high
12721 uptake skewness low & irregularity very low & dispersion s1 low to very high
1541 irregularity low & Energy ptime4 low to medium
12632 Area Under Uptake curve(in) very low to high & Variance ptime1 very low & Energy ptime4 very low to high & dispersion s16 low to very high & 2nd post-SE s17 low to very high & 3rd post-SE s6 low to very high
1073 circularity high & T2w radial gradient variance medium to high & T2w radial gradient variance very low to high
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
515 SER(in) low & max Radial gradient medium to high & Sum variance ptime2 very low to high & 1st post-SE s10 low to very high
1338 irregularity low & Energy ptime4 low to medium
7750 circularity high & Sum average ptime1 low
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
3902 circularity high & T2w radial gradient variance medium to high
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
726 SER(in) low & T2w Energy medium to high
5658 SER(rim) low & Difference variance ptime1 low & T2w Correlation low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
4809 enhancement-variance decreasing rate(rim) high & Sum variance ptime2 low to medium & last post-SE s10 medium to high
9527 max relative signal enhancement(rim) medium to high & change in Variance of spatial Margin Gradient very high
pred prob sumtempProb
1233 NC 0.4810853, 0.2872408, 0.4052440, 0.3282516 0.3754554
12721 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
1541 NC 0.4792871, 0.2735542 0.3764207
12632 NC 0.4755872, 0.5433402, 0.4788114, 0.4381729, 0.4557238, 0.5067061 0.4830569
1073 NC 0.6781025, 0.4757408, 0.5921319 0.5819917
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
515 NC 0.2902278, 0.4509106, 0.3336921, 0.3700841 0.3612286
1338 NC 0.4991863, 0.2996197 0.399403
7750 NC 0.5779883, 0.4539037 0.515946
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
3902 NC 0.5514954, 0.4847561 0.5181258
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
726 NC 0.4881946, 0.2745578 0.3813762
5658 NC 0.5505793, 0.3818076, 0.5017071 0.4780313
750 NC 0.4236079, 0.2408969 0.3322524
4809 NC 0.4806604, 0.4285987, 0.5949174 0.5013922
9527 NC 0.6236805, 0.4747261 0.5492033
Ruletype
1233 T1wdynamic & T1wmorphology & T1wtexture
12721 T1wdynamic & T1wmorphology & dispersion
1541 T1wmorphology & T1wtexture
12632 T1wdynamic & T1wtexture & dispersion & single-time-Enh
1073 T1wmorphology & T2w
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
515 T1wdynamic & T1wmorphology & T1wtexture & single-time-Enh
1338 T1wmorphology & T1wtexture
7750 T1wmorphology & T1wtexture
5547 T1wmorphology & T1wtexture & dispersion & T2w
3902 T1wmorphology & T2w
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
726 T1wdynamic & T2w
5658 T1wdynamic & T1wtexture & T2w
750 T1wmorphology & T1wtexture
4809 T1wdynamic & T1wtexture & single-time-Enh
9527 T1wdynamic & T1wmorphology
[1] 15
len freq err
1233 4 0.066 0.028
12721 3 0.127 0.043
1541 2 0.162 0.0570000000000001
12632 6 0.096 0.0580000000000001
1073 3 0.06 0.0610000000000001
1996 2 0.184 0.069
883 2 0.197 0.073
515 4 0.195 0.074
1338 2 0.193 0.077
7111 4 0.094 0.077
7750 2 0.091 0.082
5547 5 0.17 0.087
3902 2 0.124 0.088
8424 3 0.185 0.09
6375 4 0.202 0.092
726 2 0.215 0.093
5658 3 0.177 0.093
750 2 0.25 0.094
9527 2 0.057 0.097
condition
1233 enhancement-variance increasing rate(rim) low to medium & Max Margin Gradient low & Entropy ptime1 low & Sum average ptime2 very low to high
12721 uptake skewness low & irregularity very low & dispersion s1 low to very high
1541 irregularity low & Energy ptime4 low to medium
12632 Area Under Uptake curve(in) very low to high & Variance ptime1 very low & Energy ptime4 very low to high & dispersion s16 low to very high & 2nd post-SE s17 low to very high & 3rd post-SE s6 low to very high
1073 circularity high & T2w radial gradient variance medium to high & T2w radial gradient variance very low to high
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
515 SER(in) low & max Radial gradient medium to high & Sum variance ptime2 very low to high & 1st post-SE s10 low to very high
1338 irregularity low & Energy ptime4 low to medium
7111 Initial Uptake slope(in) low to medium & Curvature at Time-to-peak(in) low to very high & dispersion s10 low to very high & 2nd post-SE s11 high
7750 circularity high & Sum average ptime1 low
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
3902 circularity high & T2w radial gradient variance medium to high
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
726 SER(in) low & T2w Energy medium to high
5658 SER(rim) low & Difference variance ptime1 low & T2w Correlation low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
9527 max relative signal enhancement(rim) medium to high & change in Variance of spatial Margin Gradient very high
pred prob sumtempProb
1233 NC 0.4810853, 0.2872408, 0.4052440, 0.3282516 0.3754554
12721 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
1541 NC 0.4792871, 0.2735542 0.3764207
12632 NC 0.4755872, 0.5433402, 0.4788114, 0.4381729, 0.4557238, 0.5067061 0.4830569
1073 NC 0.6781025, 0.4757408, 0.5921319 0.5819917
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
515 NC 0.2902278, 0.4509106, 0.3336921, 0.3700841 0.3612286
1338 NC 0.4991863, 0.2996197 0.399403
7111 NC 0.4452511, 0.5362599, 0.3412410, 0.4844197 0.4517929
7750 NC 0.5779883, 0.4539037 0.515946
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
3902 NC 0.5514954, 0.4847561 0.5181258
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
726 NC 0.4881946, 0.2745578 0.3813762
5658 NC 0.5505793, 0.3818076, 0.5017071 0.4780313
750 NC 0.4236079, 0.2408969 0.3322524
9527 NC 0.6236805, 0.4747261 0.5492033
Ruletype
1233 T1wdynamic & T1wmorphology & T1wtexture
12721 T1wdynamic & T1wmorphology & dispersion
1541 T1wmorphology & T1wtexture
12632 T1wdynamic & T1wtexture & dispersion & single-time-Enh
1073 T1wmorphology & T2w
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
515 T1wdynamic & T1wmorphology & T1wtexture & single-time-Enh
1338 T1wmorphology & T1wtexture
7111 T1wdynamic & dispersion & single-time-Enh
7750 T1wmorphology & T1wtexture
5547 T1wmorphology & T1wtexture & dispersion & T2w
3902 T1wmorphology & T2w
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
726 T1wdynamic & T2w
5658 T1wdynamic & T1wtexture & T2w
750 T1wmorphology & T1wtexture
9527 T1wdynamic & T1wmorphology
[1] 16
len freq err
10203 4 0.057 0.032
1342 3 0.053 0.034
1593 6 0.047 0.038
4833 5 0.038 0.048
1541 2 0.162 0.0570000000000001
1996 2 0.184 0.069
883 2 0.197 0.073
1338 2 0.193 0.077
723 3 0.108 0.083
5547 5 0.17 0.087
8534 4 0.103 0.088
6375 4 0.202 0.092
750 2 0.25 0.094
2209 3 0.076 0.095
condition
10203 Max Radial gradient variance very low & Sum average ptime1 medium to high & 1st post-SE s16 low to very high & T2w Inverse difference moment low to very high
1342 enhancement-variance at first time-point(in) very low & irregularity very low & max T2w SI low to very high
1593 circularity high & dispersion s5 low to very high & dispersion s10 low to very high & 3rd post-SE s7 very low to high & 3rd post-SE s12 medium to high & last post-SE s17 low
4833 Max Radial gradient variance very low & Sum average ptime3 medium to high & Entropy ptime4 very low to high & dispersion s18 low & 2nd post-SE s15 very low to high
1541 irregularity low & Energy ptime4 low to medium
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
1338 irregularity low & Energy ptime4 low to medium
723 irregularity low to medium & 3rd post-SE s10 low to very high & 3rd post-SE s16 low
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
8534 SER(rim) very low to high & dispersion s1 very low & dispersion s14 low & 2nd post-SE s16 high
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
2209 enhancement-variance increasing rate(rim) low to medium & dispersion s16 very low & last post-SE s8 high
pred prob sumtempProb
10203 NC 0.6231637, 0.2928371, 0.5364463, 0.5693335 0.5054452
1342 NC 0.4848342, 0.5546800, 0.6219773 0.5538305
1593 NC 0.6372325, 0.7199635, 0.4684946, 0.4917864, 0.5568750, 0.4652017 0.5565923
4833 NC 0.4289456, 0.6226296, 0.5110246, 0.5385531, 0.4767274 0.5155761
1541 NC 0.4792871, 0.2735542 0.3764207
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
1338 NC 0.4991863, 0.2996197 0.399403
723 NC 0.5052503, 0.4047316, 0.3668232 0.4256017
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
8534 NC 0.4581848, 0.5217262, 0.6139028, 0.5050821 0.524724
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
750 NC 0.4236079, 0.2408969 0.3322524
2209 NC 0.3132262, 0.5008952, 0.5531483 0.4557566
Ruletype
10203 T1wmorphology & T1wtexture & single-time-Enh & T2w
1342 T1wdynamic & T1wmorphology & T2w
1593 T1wmorphology & dispersion & single-time-Enh
4833 T1wmorphology & T1wtexture & dispersion & single-time-Enh
1541 T1wmorphology & T1wtexture
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
1338 T1wmorphology & T1wtexture
723 T1wmorphology & single-time-Enh
5547 T1wmorphology & T1wtexture & dispersion & T2w
8534 T1wdynamic & dispersion & single-time-Enh
6375 T1wmorphology & dispersion & T2w
750 T1wmorphology & T1wtexture
2209 T1wdynamic & dispersion & single-time-Enh
[1] 19
len freq err
1342 3 0.053 0.034
12721 3 0.127 0.043
1541 2 0.162 0.0570000000000001
1996 2 0.184 0.069
2076 2 0.052 0.071
883 2 0.197 0.073
515 4 0.195 0.074
1338 2 0.193 0.077
723 3 0.108 0.083
6375 4 0.202 0.092
726 2 0.215 0.093
750 2 0.25 0.094
5386 3 0.116 0.095
condition
1342 enhancement-variance at first time-point(in) very low & irregularity very low & max T2w SI low to very high
12721 uptake skewness low & irregularity very low & dispersion s1 low to very high
1541 irregularity low & Energy ptime4 low to medium
1996 irregularity low & Energy ptime4 low to medium
2076 SER(in) low & enhancement-variance increasing rate(in) very low
883 irregularity low & Energy ptime4 low to medium
515 SER(in) low & max Radial gradient medium to high & Sum variance ptime2 very low to high & 1st post-SE s10 low to very high
1338 irregularity low & Energy ptime4 low to medium
723 irregularity low to medium & 3rd post-SE s10 low to very high & 3rd post-SE s16 low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
726 SER(in) low & T2w Energy medium to high
750 irregularity low & Inverse difference moment ptime4 low to medium
5386 SER(in) very low & enhancement-variance increasing rate(in) very low to high & enhancement-variance decreasing rate(rim) very low to high
pred prob sumtempProb
1342 NC 0.4848342, 0.5546800, 0.6219773 0.5538305
12721 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
1541 NC 0.4792871, 0.2735542 0.3764207
1996 NC 0.5007048, 0.3009807 0.4008427
2076 NC 0.6114913, 0.4662233 0.5388573
883 NC 0.4694149, 0.2405692 0.3549921
515 NC 0.2902278, 0.4509106, 0.3336921, 0.3700841 0.3612286
1338 NC 0.4991863, 0.2996197 0.399403
723 NC 0.5052503, 0.4047316, 0.3668232 0.4256017
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
726 NC 0.4881946, 0.2745578 0.3813762
750 NC 0.4236079, 0.2408969 0.3322524
5386 NC 0.5192031, 0.5443866, 0.4975629 0.5203842
Ruletype
1342 T1wdynamic & T1wmorphology & T2w
12721 T1wdynamic & T1wmorphology & dispersion
1541 T1wmorphology & T1wtexture
1996 T1wmorphology & T1wtexture
2076 T1wdynamic
883 T1wmorphology & T1wtexture
515 T1wdynamic & T1wmorphology & T1wtexture & single-time-Enh
1338 T1wmorphology & T1wtexture
723 T1wmorphology & single-time-Enh
6375 T1wmorphology & dispersion & T2w
726 T1wdynamic & T2w
750 T1wmorphology & T1wtexture
5386 T1wdynamic
[1] 21
len freq err
9109 4 0.041 0
1233 4 0.066 0.028
1342 3 0.053 0.034
12721 3 0.127 0.043
1541 2 0.162 0.0570000000000001
1996 2 0.184 0.069
2076 2 0.052 0.071
883 2 0.197 0.073
515 4 0.195 0.074
5316 5 0.168 0.075
1338 2 0.193 0.077
7750 2 0.091 0.082
723 3 0.108 0.083
5547 5 0.17 0.087
8424 3 0.185 0.09
6375 4 0.202 0.092
726 2 0.215 0.093
5658 3 0.177 0.093
750 2 0.25 0.094
722 4 0.136 0.095
condition
9109 Initial Uptake slope(in) low & uptake average high & 1st post-SE s15 low to very high & 1st post-SE s16 low to very high
1233 enhancement-variance increasing rate(rim) low to medium & Max Margin Gradient low & Entropy ptime1 low & Sum average ptime2 very low to high
1342 enhancement-variance at first time-point(in) very low & irregularity very low & max T2w SI low to very high
12721 uptake skewness low & irregularity very low & dispersion s1 low to very high
1541 irregularity low & Energy ptime4 low to medium
1996 irregularity low & Energy ptime4 low to medium
2076 SER(in) low & enhancement-variance increasing rate(in) very low
883 irregularity low & Energy ptime4 low to medium
515 SER(in) low & max Radial gradient medium to high & Sum variance ptime2 very low to high & 1st post-SE s10 low to very high
5316 Initial Uptake slope(in) low & uptake average low to very high & 1st post-SE s10 low to very high & T2w std SI low to medium & T2w margin gradient variance very low to high
1338 irregularity low & Energy ptime4 low to medium
7750 circularity high & Sum average ptime1 low
723 irregularity low to medium & 3rd post-SE s10 low to very high & 3rd post-SE s16 low
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
726 SER(in) low & T2w Energy medium to high
5658 SER(rim) low & Difference variance ptime1 low & T2w Correlation low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
722 uptake average high & irregularity low to medium & 1st post-SE s8 low to medium & T2w radial gradient variance low
pred prob sumtempProb
9109 NC 0.6920559, 0.4833696, 0.7240647, 0.5912338 0.622681
1233 NC 0.4810853, 0.2872408, 0.4052440, 0.3282516 0.3754554
1342 NC 0.4848342, 0.5546800, 0.6219773 0.5538305
12721 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
1541 NC 0.4792871, 0.2735542 0.3764207
1996 NC 0.5007048, 0.3009807 0.4008427
2076 NC 0.6114913, 0.4662233 0.5388573
883 NC 0.4694149, 0.2405692 0.3549921
515 NC 0.2902278, 0.4509106, 0.3336921, 0.3700841 0.3612286
5316 NC 0.4508790, 0.4713496, 0.5509649, 0.5310208, 0.5073532 0.5023135
1338 NC 0.4991863, 0.2996197 0.399403
7750 NC 0.5779883, 0.4539037 0.515946
723 NC 0.5052503, 0.4047316, 0.3668232 0.4256017
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
726 NC 0.4881946, 0.2745578 0.3813762
5658 NC 0.5505793, 0.3818076, 0.5017071 0.4780313
750 NC 0.4236079, 0.2408969 0.3322524
722 NC 0.4364043, 0.5007630, 0.5571853, 0.4727589 0.4917779
Ruletype
9109 T1wdynamic & single-time-Enh
1233 T1wdynamic & T1wmorphology & T1wtexture
1342 T1wdynamic & T1wmorphology & T2w
12721 T1wdynamic & T1wmorphology & dispersion
1541 T1wmorphology & T1wtexture
1996 T1wmorphology & T1wtexture
2076 T1wdynamic
883 T1wmorphology & T1wtexture
515 T1wdynamic & T1wmorphology & T1wtexture & single-time-Enh
5316 T1wdynamic & single-time-Enh & T2w
1338 T1wmorphology & T1wtexture
7750 T1wmorphology & T1wtexture
723 T1wmorphology & single-time-Enh
5547 T1wmorphology & T1wtexture & dispersion & T2w
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
726 T1wdynamic & T2w
5658 T1wdynamic & T1wtexture & T2w
750 T1wmorphology & T1wtexture
722 T1wdynamic & T1wmorphology & single-time-Enh & T2w
[1] 23
len freq err
12632 6 0.096 0.0580000000000001
1073 3 0.06 0.0610000000000001
7750 2 0.091 0.082
3902 2 0.124 0.088
6375 4 0.202 0.092
condition
12632 Area Under Uptake curve(in) very low to high & Variance ptime1 very low & Energy ptime4 very low to high & dispersion s16 low to very high & 2nd post-SE s17 low to very high & 3rd post-SE s6 low to very high
1073 circularity high & T2w radial gradient variance medium to high & T2w radial gradient variance very low to high
7750 circularity high & Sum average ptime1 low
3902 circularity high & T2w radial gradient variance medium to high
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
pred prob sumtempProb
12632 NC 0.4755872, 0.5433402, 0.4788114, 0.4381729, 0.4557238, 0.5067061 0.4830569
1073 NC 0.6781025, 0.4757408, 0.5921319 0.5819917
7750 NC 0.5779883, 0.4539037 0.515946
3902 NC 0.5514954, 0.4847561 0.5181258
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
Ruletype
12632 T1wdynamic & T1wtexture & dispersion & single-time-Enh
1073 T1wmorphology & T2w
7750 T1wmorphology & T1wtexture
3902 T1wmorphology & T2w
6375 T1wmorphology & dispersion & T2w
[1] 26
len freq err
9109 4 0.041 0
4833 5 0.038 0.048
1541 2 0.162 0.0570000000000001
1996 2 0.184 0.069
2076 2 0.052 0.071
883 2 0.197 0.073
515 4 0.195 0.074
5316 5 0.168 0.075
1338 2 0.193 0.077
7111 4 0.094 0.077
5547 5 0.17 0.087
8534 4 0.103 0.088
6375 4 0.202 0.092
726 2 0.215 0.093
750 2 0.25 0.094
2209 3 0.076 0.095
722 4 0.136 0.095
condition
9109 Initial Uptake slope(in) low & uptake average high & 1st post-SE s15 low to very high & 1st post-SE s16 low to very high
4833 Max Radial gradient variance very low & Sum average ptime3 medium to high & Entropy ptime4 very low to high & dispersion s18 low & 2nd post-SE s15 very low to high
1541 irregularity low & Energy ptime4 low to medium
1996 irregularity low & Energy ptime4 low to medium
2076 SER(in) low & enhancement-variance increasing rate(in) very low
883 irregularity low & Energy ptime4 low to medium
515 SER(in) low & max Radial gradient medium to high & Sum variance ptime2 very low to high & 1st post-SE s10 low to very high
5316 Initial Uptake slope(in) low & uptake average low to very high & 1st post-SE s10 low to very high & T2w std SI low to medium & T2w margin gradient variance very low to high
1338 irregularity low & Energy ptime4 low to medium
7111 Initial Uptake slope(in) low to medium & Curvature at Time-to-peak(in) low to very high & dispersion s10 low to very high & 2nd post-SE s11 high
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
8534 SER(rim) very low to high & dispersion s1 very low & dispersion s14 low & 2nd post-SE s16 high
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
726 SER(in) low & T2w Energy medium to high
750 irregularity low & Inverse difference moment ptime4 low to medium
2209 enhancement-variance increasing rate(rim) low to medium & dispersion s16 very low & last post-SE s8 high
722 uptake average high & irregularity low to medium & 1st post-SE s8 low to medium & T2w radial gradient variance low
pred prob sumtempProb
9109 NC 0.6920559, 0.4833696, 0.7240647, 0.5912338 0.622681
4833 NC 0.4289456, 0.6226296, 0.5110246, 0.5385531, 0.4767274 0.5155761
1541 NC 0.4792871, 0.2735542 0.3764207
1996 NC 0.5007048, 0.3009807 0.4008427
2076 NC 0.6114913, 0.4662233 0.5388573
883 NC 0.4694149, 0.2405692 0.3549921
515 NC 0.2902278, 0.4509106, 0.3336921, 0.3700841 0.3612286
5316 NC 0.4508790, 0.4713496, 0.5509649, 0.5310208, 0.5073532 0.5023135
1338 NC 0.4991863, 0.2996197 0.399403
7111 NC 0.4452511, 0.5362599, 0.3412410, 0.4844197 0.4517929
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
8534 NC 0.4581848, 0.5217262, 0.6139028, 0.5050821 0.524724
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
726 NC 0.4881946, 0.2745578 0.3813762
750 NC 0.4236079, 0.2408969 0.3322524
2209 NC 0.3132262, 0.5008952, 0.5531483 0.4557566
722 NC 0.4364043, 0.5007630, 0.5571853, 0.4727589 0.4917779
Ruletype
9109 T1wdynamic & single-time-Enh
4833 T1wmorphology & T1wtexture & dispersion & single-time-Enh
1541 T1wmorphology & T1wtexture
1996 T1wmorphology & T1wtexture
2076 T1wdynamic
883 T1wmorphology & T1wtexture
515 T1wdynamic & T1wmorphology & T1wtexture & single-time-Enh
5316 T1wdynamic & single-time-Enh & T2w
1338 T1wmorphology & T1wtexture
7111 T1wdynamic & dispersion & single-time-Enh
5547 T1wmorphology & T1wtexture & dispersion & T2w
8534 T1wdynamic & dispersion & single-time-Enh
6375 T1wmorphology & dispersion & T2w
726 T1wdynamic & T2w
750 T1wmorphology & T1wtexture
2209 T1wdynamic & dispersion & single-time-Enh
722 T1wdynamic & T1wmorphology & single-time-Enh & T2w
[1] 30
len freq err
1541 2 0.162 0.0570000000000001
12632 6 0.096 0.0580000000000001
1996 2 0.184 0.069
883 2 0.197 0.073
1338 2 0.193 0.077
7750 2 0.091 0.082
5547 5 0.17 0.087
3902 2 0.124 0.088
6375 4 0.202 0.092
750 2 0.25 0.094
4809 3 0.095 0.096
condition
1541 irregularity low & Energy ptime4 low to medium
12632 Area Under Uptake curve(in) very low to high & Variance ptime1 very low & Energy ptime4 very low to high & dispersion s16 low to very high & 2nd post-SE s17 low to very high & 3rd post-SE s6 low to very high
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
1338 irregularity low & Energy ptime4 low to medium
7750 circularity high & Sum average ptime1 low
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
3902 circularity high & T2w radial gradient variance medium to high
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
4809 enhancement-variance decreasing rate(rim) high & Sum variance ptime2 low to medium & last post-SE s10 medium to high
pred prob sumtempProb
1541 NC 0.4792871, 0.2735542 0.3764207
12632 NC 0.4755872, 0.5433402, 0.4788114, 0.4381729, 0.4557238, 0.5067061 0.4830569
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
1338 NC 0.4991863, 0.2996197 0.399403
7750 NC 0.5779883, 0.4539037 0.515946
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
3902 NC 0.5514954, 0.4847561 0.5181258
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
750 NC 0.4236079, 0.2408969 0.3322524
4809 NC 0.4806604, 0.4285987, 0.5949174 0.5013922
Ruletype
1541 T1wmorphology & T1wtexture
12632 T1wdynamic & T1wtexture & dispersion & single-time-Enh
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
1338 T1wmorphology & T1wtexture
7750 T1wmorphology & T1wtexture
5547 T1wmorphology & T1wtexture & dispersion & T2w
3902 T1wmorphology & T2w
6375 T1wmorphology & dispersion & T2w
750 T1wmorphology & T1wtexture
4809 T1wdynamic & T1wtexture & single-time-Enh
[1] 32
len freq err
12721 3 0.127 0.043
5316 5 0.168 0.075
7111 4 0.094 0.077
8424 3 0.185 0.09
6375 4 0.202 0.092
5658 3 0.177 0.093
750 2 0.25 0.094
4809 3 0.095 0.096
condition
12721 uptake skewness low & irregularity very low & dispersion s1 low to very high
5316 Initial Uptake slope(in) low & uptake average low to very high & 1st post-SE s10 low to very high & T2w std SI low to medium & T2w margin gradient variance very low to high
7111 Initial Uptake slope(in) low to medium & Curvature at Time-to-peak(in) low to very high & dispersion s10 low to very high & 2nd post-SE s11 high
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
5658 SER(rim) low & Difference variance ptime1 low & T2w Correlation low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
4809 enhancement-variance decreasing rate(rim) high & Sum variance ptime2 low to medium & last post-SE s10 medium to high
pred prob sumtempProb
12721 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
5316 NC 0.4508790, 0.4713496, 0.5509649, 0.5310208, 0.5073532 0.5023135
7111 NC 0.4452511, 0.5362599, 0.3412410, 0.4844197 0.4517929
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
5658 NC 0.5505793, 0.3818076, 0.5017071 0.4780313
750 NC 0.4236079, 0.2408969 0.3322524
4809 NC 0.4806604, 0.4285987, 0.5949174 0.5013922
Ruletype
12721 T1wdynamic & T1wmorphology & dispersion
5316 T1wdynamic & single-time-Enh & T2w
7111 T1wdynamic & dispersion & single-time-Enh
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
5658 T1wdynamic & T1wtexture & T2w
750 T1wmorphology & T1wtexture
4809 T1wdynamic & T1wtexture & single-time-Enh
[1] 33
len freq err
10203 4 0.057 0.032
4971 4 0.055 0.033
12721 3 0.127 0.043
1541 2 0.162 0.0570000000000001
715 3 0.08 0.0679999999999999
1996 2 0.184 0.069
883 2 0.197 0.073
1338 2 0.193 0.077
8424 3 0.185 0.09
6375 4 0.202 0.092
750 2 0.25 0.094
condition
10203 Max Radial gradient variance very low & Sum average ptime1 medium to high & 1st post-SE s16 low to very high & T2w Inverse difference moment low to very high
4971 min uptake very low to high & mean 3D Sharpness of lesion margin very low & Energy ptime4 low to medium & dispersion s16 low
12721 uptake skewness low & irregularity very low & dispersion s1 low to very high
1541 irregularity low & Energy ptime4 low to medium
715 uptake average high & Inverse difference moment ptime2 low to medium & 1st post-SE s8 high
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
1338 irregularity low & Energy ptime4 low to medium
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
pred prob sumtempProb
10203 NC 0.6231637, 0.2928371, 0.5364463, 0.5693335 0.5054452
4971 NC 0.4686661, 0.3111970, 0.4932763, 0.4507027 0.4309605
12721 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
1541 NC 0.4792871, 0.2735542 0.3764207
715 C 0.5436611, 0.6397459, 0.5003391 0.5612487
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
1338 NC 0.4991863, 0.2996197 0.399403
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
750 NC 0.4236079, 0.2408969 0.3322524
Ruletype
10203 T1wmorphology & T1wtexture & single-time-Enh & T2w
4971 T1wdynamic & T1wmorphology & T1wtexture & dispersion
12721 T1wdynamic & T1wmorphology & dispersion
1541 T1wmorphology & T1wtexture
715 T1wdynamic & T1wtexture & single-time-Enh
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
1338 T1wmorphology & T1wtexture
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
750 T1wmorphology & T1wtexture
[1] 39
len freq err
10203 4 0.057 0.032
7103 2 0.044 0.042
1578 3 0.057 0.0649999999999999
3314 5 0.07 0.077
1977 2 0.045 0.08
8534 4 0.103 0.088
6375 4 0.202 0.092
2931 3 0.038 0.095
condition
10203 Max Radial gradient variance very low & Sum average ptime1 medium to high & 1st post-SE s16 low to very high & T2w Inverse difference moment low to very high
7103 irregularity very low & T2w radial gradient variance medium to high
1578 irregularity very low & Difference variance ptime3 very low to high & T2w radial gradient variance medium to high
3314 SER(rim) very low to high & dispersion s14 very low & dispersion s15 very low to high & 1st post-SE s4 low to very high & T2w Entropy low
1977 dispersion s5 very low & 1st post-SE s11 low
8534 SER(rim) very low to high & dispersion s1 very low & dispersion s14 low & 2nd post-SE s16 high
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
2931 Rate of signal increase(rim) very low & dispersion s17 low to very high & T2w mean SI low to very high
pred prob sumtempProb
10203 NC 0.6231637, 0.2928371, 0.5364463, 0.5693335 0.5054452
7103 NC 0.5748740, 0.4661645 0.5205192
1578 NC 0.5914519, 0.4717202, 0.4894149 0.517529
3314 NC 0.4499065, 0.4352475, 0.4759258, 0.4943733, 0.5792785 0.4869463
1977 NC 0.4735013, 0.6948949 0.5841981
8534 NC 0.4581848, 0.5217262, 0.6139028, 0.5050821 0.524724
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
2931 NC 0.5582364, 0.5165599, 0.5742535 0.5496832
Ruletype
10203 T1wmorphology & T1wtexture & single-time-Enh & T2w
7103 T1wmorphology & T2w
1578 T1wmorphology & T1wtexture & T2w
3314 T1wdynamic & dispersion & single-time-Enh & T2w
1977 dispersion & single-time-Enh
8534 T1wdynamic & dispersion & single-time-Enh
6375 T1wmorphology & dispersion & T2w
2931 T1wdynamic & dispersion & T2w
[1] 44
len freq err
1233 4 0.066 0.028
10158 2 0.048 0.038
7103 2 0.044 0.042
1073 3 0.06 0.0610000000000001
1578 3 0.057 0.0649999999999999
7111 4 0.094 0.077
7750 2 0.091 0.082
5547 5 0.17 0.087
3902 2 0.124 0.088
6375 4 0.202 0.092
5658 3 0.177 0.093
750 2 0.25 0.094
5386 3 0.116 0.095
9527 2 0.057 0.097
condition
1233 enhancement-variance increasing rate(rim) low to medium & Max Margin Gradient low & Entropy ptime1 low & Sum average ptime2 very low to high
10158 Energy ptime1 very low to high & Entropy ptime2 very low
7103 irregularity very low & T2w radial gradient variance medium to high
1073 circularity high & T2w radial gradient variance medium to high & T2w radial gradient variance very low to high
1578 irregularity very low & Difference variance ptime3 very low to high & T2w radial gradient variance medium to high
7111 Initial Uptake slope(in) low to medium & Curvature at Time-to-peak(in) low to very high & dispersion s10 low to very high & 2nd post-SE s11 high
7750 circularity high & Sum average ptime1 low
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
3902 circularity high & T2w radial gradient variance medium to high
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
5658 SER(rim) low & Difference variance ptime1 low & T2w Correlation low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
5386 SER(in) very low & enhancement-variance increasing rate(in) very low to high & enhancement-variance decreasing rate(rim) very low to high
9527 max relative signal enhancement(rim) medium to high & change in Variance of spatial Margin Gradient very high
pred prob sumtempProb
1233 NC 0.4810853, 0.2872408, 0.4052440, 0.3282516 0.3754554
10158 NC 0.5127610, 0.4835754 0.4981682
7103 NC 0.5748740, 0.4661645 0.5205192
1073 NC 0.6781025, 0.4757408, 0.5921319 0.5819917
1578 NC 0.5914519, 0.4717202, 0.4894149 0.517529
7111 NC 0.4452511, 0.5362599, 0.3412410, 0.4844197 0.4517929
7750 NC 0.5779883, 0.4539037 0.515946
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
3902 NC 0.5514954, 0.4847561 0.5181258
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
5658 NC 0.5505793, 0.3818076, 0.5017071 0.4780313
750 NC 0.4236079, 0.2408969 0.3322524
5386 NC 0.5192031, 0.5443866, 0.4975629 0.5203842
9527 NC 0.6236805, 0.4747261 0.5492033
Ruletype
1233 T1wdynamic & T1wmorphology & T1wtexture
10158 T1wtexture
7103 T1wmorphology & T2w
1073 T1wmorphology & T2w
1578 T1wmorphology & T1wtexture & T2w
7111 T1wdynamic & dispersion & single-time-Enh
7750 T1wmorphology & T1wtexture
5547 T1wmorphology & T1wtexture & dispersion & T2w
3902 T1wmorphology & T2w
6375 T1wmorphology & dispersion & T2w
5658 T1wdynamic & T1wtexture & T2w
750 T1wmorphology & T1wtexture
5386 T1wdynamic
9527 T1wdynamic & T1wmorphology
[1] 50
len freq err
12721 3 0.127 0.043
1541 2 0.162 0.0570000000000001
6591 4 0.031 0.0590000000000001
1996 2 0.184 0.069
883 2 0.197 0.073
515 4 0.195 0.074
1338 2 0.193 0.077
8424 3 0.185 0.09
6375 4 0.202 0.092
726 2 0.215 0.093
750 2 0.25 0.094
condition
12721 uptake skewness low & irregularity very low & dispersion s1 low to very high
1541 irregularity low & Energy ptime4 low to medium
6591 Rate of signal increase(in) low & Rate of signal increase(in) medium to high & 1st post-SE s15 low to very high & last post-SE s8 low to very high
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
515 SER(in) low & max Radial gradient medium to high & Sum variance ptime2 very low to high & 1st post-SE s10 low to very high
1338 irregularity low & Energy ptime4 low to medium
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
726 SER(in) low & T2w Energy medium to high
750 irregularity low & Inverse difference moment ptime4 low to medium
pred prob sumtempProb
12721 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
1541 NC 0.4792871, 0.2735542 0.3764207
6591 NC 0.5271721, 0.3903370, 0.5439983, 0.4908403 0.488087
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
515 NC 0.2902278, 0.4509106, 0.3336921, 0.3700841 0.3612286
1338 NC 0.4991863, 0.2996197 0.399403
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
726 NC 0.4881946, 0.2745578 0.3813762
750 NC 0.4236079, 0.2408969 0.3322524
Ruletype
12721 T1wdynamic & T1wmorphology & dispersion
1541 T1wmorphology & T1wtexture
6591 T1wdynamic & single-time-Enh
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
515 T1wdynamic & T1wmorphology & T1wtexture & single-time-Enh
1338 T1wmorphology & T1wtexture
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
726 T1wdynamic & T2w
750 T1wmorphology & T1wtexture
[1] 51
len freq err
1342 3 0.053 0.034
1593 6 0.047 0.038
10158 2 0.048 0.038
12721 3 0.127 0.043
6591 4 0.031 0.0590000000000001
3902 2 0.124 0.088
8424 3 0.185 0.09
6375 4 0.202 0.092
condition
1342 enhancement-variance at first time-point(in) very low & irregularity very low & max T2w SI low to very high
1593 circularity high & dispersion s5 low to very high & dispersion s10 low to very high & 3rd post-SE s7 very low to high & 3rd post-SE s12 medium to high & last post-SE s17 low
10158 Energy ptime1 very low to high & Entropy ptime2 very low
12721 uptake skewness low & irregularity very low & dispersion s1 low to very high
6591 Rate of signal increase(in) low & Rate of signal increase(in) medium to high & 1st post-SE s15 low to very high & last post-SE s8 low to very high
3902 circularity high & T2w radial gradient variance medium to high
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
pred prob sumtempProb
1342 NC 0.4848342, 0.5546800, 0.6219773 0.5538305
1593 NC 0.6372325, 0.7199635, 0.4684946, 0.4917864, 0.5568750, 0.4652017 0.5565923
10158 NC 0.5127610, 0.4835754 0.4981682
12721 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
6591 NC 0.5271721, 0.3903370, 0.5439983, 0.4908403 0.488087
3902 NC 0.5514954, 0.4847561 0.5181258
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
Ruletype
1342 T1wdynamic & T1wmorphology & T2w
1593 T1wmorphology & dispersion & single-time-Enh
10158 T1wtexture
12721 T1wdynamic & T1wmorphology & dispersion
6591 T1wdynamic & single-time-Enh
3902 T1wmorphology & T2w
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
[1] 54
len freq err
4971 4 0.055 0.033
1541 2 0.162 0.0570000000000001
1996 2 0.184 0.069
883 2 0.197 0.073
515 4 0.195 0.074
5316 5 0.168 0.075
1338 2 0.193 0.077
7111 4 0.094 0.077
8424 3 0.185 0.09
6375 4 0.202 0.092
726 2 0.215 0.093
750 2 0.25 0.094
4809 3 0.095 0.096
condition
4971 min uptake very low to high & mean 3D Sharpness of lesion margin very low & Energy ptime4 low to medium & dispersion s16 low
1541 irregularity low & Energy ptime4 low to medium
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
515 SER(in) low & max Radial gradient medium to high & Sum variance ptime2 very low to high & 1st post-SE s10 low to very high
5316 Initial Uptake slope(in) low & uptake average low to very high & 1st post-SE s10 low to very high & T2w std SI low to medium & T2w margin gradient variance very low to high
1338 irregularity low & Energy ptime4 low to medium
7111 Initial Uptake slope(in) low to medium & Curvature at Time-to-peak(in) low to very high & dispersion s10 low to very high & 2nd post-SE s11 high
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
726 SER(in) low & T2w Energy medium to high
750 irregularity low & Inverse difference moment ptime4 low to medium
4809 enhancement-variance decreasing rate(rim) high & Sum variance ptime2 low to medium & last post-SE s10 medium to high
pred prob sumtempProb
4971 NC 0.4686661, 0.3111970, 0.4932763, 0.4507027 0.4309605
1541 NC 0.4792871, 0.2735542 0.3764207
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
515 NC 0.2902278, 0.4509106, 0.3336921, 0.3700841 0.3612286
5316 NC 0.4508790, 0.4713496, 0.5509649, 0.5310208, 0.5073532 0.5023135
1338 NC 0.4991863, 0.2996197 0.399403
7111 NC 0.4452511, 0.5362599, 0.3412410, 0.4844197 0.4517929
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
726 NC 0.4881946, 0.2745578 0.3813762
750 NC 0.4236079, 0.2408969 0.3322524
4809 NC 0.4806604, 0.4285987, 0.5949174 0.5013922
Ruletype
4971 T1wdynamic & T1wmorphology & T1wtexture & dispersion
1541 T1wmorphology & T1wtexture
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
515 T1wdynamic & T1wmorphology & T1wtexture & single-time-Enh
5316 T1wdynamic & single-time-Enh & T2w
1338 T1wmorphology & T1wtexture
7111 T1wdynamic & dispersion & single-time-Enh
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
726 T1wdynamic & T2w
750 T1wmorphology & T1wtexture
4809 T1wdynamic & T1wtexture & single-time-Enh
[1] 55
len freq err
1593 6 0.047 0.038
12721 3 0.127 0.043
1541 2 0.162 0.0570000000000001
1996 2 0.184 0.069
883 2 0.197 0.073
1338 2 0.193 0.077
7111 4 0.094 0.077
7750 2 0.091 0.082
5547 5 0.17 0.087
8534 4 0.103 0.088
8424 3 0.185 0.09
6375 4 0.202 0.092
750 2 0.25 0.094
9527 2 0.057 0.097
condition
1593 circularity high & dispersion s5 low to very high & dispersion s10 low to very high & 3rd post-SE s7 very low to high & 3rd post-SE s12 medium to high & last post-SE s17 low
12721 uptake skewness low & irregularity very low & dispersion s1 low to very high
1541 irregularity low & Energy ptime4 low to medium
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
1338 irregularity low & Energy ptime4 low to medium
7111 Initial Uptake slope(in) low to medium & Curvature at Time-to-peak(in) low to very high & dispersion s10 low to very high & 2nd post-SE s11 high
7750 circularity high & Sum average ptime1 low
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
8534 SER(rim) very low to high & dispersion s1 very low & dispersion s14 low & 2nd post-SE s16 high
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
9527 max relative signal enhancement(rim) medium to high & change in Variance of spatial Margin Gradient very high
pred prob sumtempProb
1593 NC 0.6372325, 0.7199635, 0.4684946, 0.4917864, 0.5568750, 0.4652017 0.5565923
12721 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
1541 NC 0.4792871, 0.2735542 0.3764207
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
1338 NC 0.4991863, 0.2996197 0.399403
7111 NC 0.4452511, 0.5362599, 0.3412410, 0.4844197 0.4517929
7750 NC 0.5779883, 0.4539037 0.515946
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
8534 NC 0.4581848, 0.5217262, 0.6139028, 0.5050821 0.524724
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
750 NC 0.4236079, 0.2408969 0.3322524
9527 NC 0.6236805, 0.4747261 0.5492033
Ruletype
1593 T1wmorphology & dispersion & single-time-Enh
12721 T1wdynamic & T1wmorphology & dispersion
1541 T1wmorphology & T1wtexture
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
1338 T1wmorphology & T1wtexture
7111 T1wdynamic & dispersion & single-time-Enh
7750 T1wmorphology & T1wtexture
5547 T1wmorphology & T1wtexture & dispersion & T2w
8534 T1wdynamic & dispersion & single-time-Enh
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
750 T1wmorphology & T1wtexture
9527 T1wdynamic & T1wmorphology
[1] 57
len freq err
1593 6 0.047 0.038
12721 3 0.127 0.043
2822 2 0.071 0.051
1541 2 0.162 0.0570000000000001
1073 3 0.06 0.0610000000000001
1996 2 0.184 0.069
883 2 0.197 0.073
1338 2 0.193 0.077
5547 5 0.17 0.087
3902 2 0.124 0.088
6375 4 0.202 0.092
750 2 0.25 0.094
condition
1593 circularity high & dispersion s5 low to very high & dispersion s10 low to very high & 3rd post-SE s7 very low to high & 3rd post-SE s12 medium to high & last post-SE s17 low
12721 uptake skewness low & irregularity very low & dispersion s1 low to very high
2822 3rd post-SE s10 low to very high & last post-SE s11 very low
1541 irregularity low & Energy ptime4 low to medium
1073 circularity high & T2w radial gradient variance medium to high & T2w radial gradient variance very low to high
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
1338 irregularity low & Energy ptime4 low to medium
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
3902 circularity high & T2w radial gradient variance medium to high
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
pred prob sumtempProb
1593 NC 0.6372325, 0.7199635, 0.4684946, 0.4917864, 0.5568750, 0.4652017 0.5565923
12721 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
2822 NC 0.5144900, 0.4830707 0.4987804
1541 NC 0.4792871, 0.2735542 0.3764207
1073 NC 0.6781025, 0.4757408, 0.5921319 0.5819917
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
1338 NC 0.4991863, 0.2996197 0.399403
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
3902 NC 0.5514954, 0.4847561 0.5181258
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
750 NC 0.4236079, 0.2408969 0.3322524
Ruletype
1593 T1wmorphology & dispersion & single-time-Enh
12721 T1wdynamic & T1wmorphology & dispersion
2822 single-time-Enh
1541 T1wmorphology & T1wtexture
1073 T1wmorphology & T2w
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
1338 T1wmorphology & T1wtexture
5547 T1wmorphology & T1wtexture & dispersion & T2w
3902 T1wmorphology & T2w
6375 T1wmorphology & dispersion & T2w
750 T1wmorphology & T1wtexture
[1] 64
len freq err
1233 4 0.066 0.028
1541 2 0.162 0.0570000000000001
12632 6 0.096 0.0580000000000001
1996 2 0.184 0.069
883 2 0.197 0.073
1338 2 0.193 0.077
7111 4 0.094 0.077
5547 5 0.17 0.087
3902 2 0.124 0.088
6375 4 0.202 0.092
750 2 0.25 0.094
condition
1233 enhancement-variance increasing rate(rim) low to medium & Max Margin Gradient low & Entropy ptime1 low & Sum average ptime2 very low to high
1541 irregularity low & Energy ptime4 low to medium
12632 Area Under Uptake curve(in) very low to high & Variance ptime1 very low & Energy ptime4 very low to high & dispersion s16 low to very high & 2nd post-SE s17 low to very high & 3rd post-SE s6 low to very high
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
1338 irregularity low & Energy ptime4 low to medium
7111 Initial Uptake slope(in) low to medium & Curvature at Time-to-peak(in) low to very high & dispersion s10 low to very high & 2nd post-SE s11 high
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
3902 circularity high & T2w radial gradient variance medium to high
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
pred prob sumtempProb
1233 NC 0.4810853, 0.2872408, 0.4052440, 0.3282516 0.3754554
1541 NC 0.4792871, 0.2735542 0.3764207
12632 NC 0.4755872, 0.5433402, 0.4788114, 0.4381729, 0.4557238, 0.5067061 0.4830569
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
1338 NC 0.4991863, 0.2996197 0.399403
7111 NC 0.4452511, 0.5362599, 0.3412410, 0.4844197 0.4517929
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
3902 NC 0.5514954, 0.4847561 0.5181258
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
750 NC 0.4236079, 0.2408969 0.3322524
Ruletype
1233 T1wdynamic & T1wmorphology & T1wtexture
1541 T1wmorphology & T1wtexture
12632 T1wdynamic & T1wtexture & dispersion & single-time-Enh
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
1338 T1wmorphology & T1wtexture
7111 T1wdynamic & dispersion & single-time-Enh
5547 T1wmorphology & T1wtexture & dispersion & T2w
3902 T1wmorphology & T2w
6375 T1wmorphology & dispersion & T2w
750 T1wmorphology & T1wtexture
print(summary(LMSIRfeatureflag))
Mode FALSE TRUE NA's
logical 45 25 0
### display
lesion_id = 10
idx = c(1:nrow(FI))[c(FI$allTestinfo.lesion_id == lesion_id)]
infoidx = allTestinfo[allTestinfo$lesion_id == lesion_id, -c(20)]
print(infoidx)
lesion_id lesionfile cad_pt_no_txt anony_dob_datetime exam_img_dicom_txt
10 10 10_0102_4755778.vtk 0102 1974-05-19 00:00:00.000000 5142
exam_a_number_txt exam_dt_datetime exam_mri_cad_status_txt
10 4755778 2009-03-19 00:00:00.000000 Benign by pathology
cad_latest_mutation_status_int exam_find_mri_mass_yn exam_find_mri_nonmass_yn
10 High Risk 1 0
exam_find_side_int proc_pt_procedure_id proc_proc_dt_datetime proc_proc_side_int
10 Right 2708 2009-04-16 00:00:00.000000 Right
proc_proc_source_int proc_proc_guid_int proc_proc_tp_int proc_lesion_comments_txt
10 Radiology MRI Vacuum Assisted Biopsy None
find_curve_int find_mri_dce_init_enh_int find_mri_dce_delay_enh_int BIRADS lesion_label
10 III N/A Washout 4 massB
lesion_diagnosis
10 FIBROCYSTIC
cat(allTestinfo[allTestinfo$lesion_id == lesion_id, c(20)])
AP Report:
(NOTE)
SURGICAL PATHOLOGY REPORT
Encounter #: 4050499R
Specimen #: S09-10059
CLINICAL INFORMATION
MRI enhancement. Rule out cancer.
SPECIMENS SUBMITTED
Right breast biopsies
DIAGNOSIS
Right breast, core biopsy:
- FIBROCYSTIC AND COLUMNAR CELL CHANGES
- FIBROEPITHELIAL LESION
COMMENT:
Sections show a benign fibroepithelial lesion with fibrocystic changes
as well as columnar cell metaplasia and hyperplasia. There are
fragments of a fibroadenoma. There is no evidence of atypia or
malignancy.
MACROSCOPIC DESCRIPTION
The specimen container is labeled with the patient name and 'right
breast samples'. The accompanying requisition matches the container' s
label. The specimen consists of approx..2 cc's of soft tan and fatty
tissue pieces which are submitted in toto in blocks 1-4.
AMM Dictated 4/17/2009
Judit Zubovits, MD, FRCPC
Report Electronically Signed
4/20/2009 15:43
print(mypresentRules(eachFITopRules[[idx]], colnames(X), fnames))
len freq err
10203 4 0.057 0.032
4971 4 0.055 0.033
12721 3 0.127 0.043
1541 2 0.162 0.0570000000000001
715 3 0.08 0.0679999999999999
1996 2 0.184 0.069
883 2 0.197 0.073
1338 2 0.193 0.077
8424 3 0.185 0.09
6375 4 0.202 0.092
750 2 0.25 0.094
condition
10203 Max Radial gradient variance very low & Sum average ptime1 medium to high & 1st post-SE s16 low to very high & T2w Inverse difference moment low to very high
4971 min uptake very low to high & mean 3D Sharpness of lesion margin very low & Energy ptime4 low to medium & dispersion s16 low
12721 uptake skewness low & irregularity very low & dispersion s1 low to very high
1541 irregularity low & Energy ptime4 low to medium
715 uptake average high & Inverse difference moment ptime2 low to medium & 1st post-SE s8 high
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
1338 irregularity low & Energy ptime4 low to medium
8424 Curvature at Time-to-peak(in) low to very high & uptake skewness low to medium & irregularity low
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
pred prob sumtempProb
10203 NC 0.6231637, 0.2928371, 0.5364463, 0.5693335 0.5054452
4971 NC 0.4686661, 0.3111970, 0.4932763, 0.4507027 0.4309605
12721 NC 0.4677355, 0.5728223, 0.2321752 0.4242443
1541 NC 0.4792871, 0.2735542 0.3764207
715 C 0.5436611, 0.6397459, 0.5003391 0.5612487
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
1338 NC 0.4991863, 0.2996197 0.399403
8424 NC 0.2901904, 0.4699588, 0.5212986 0.4271493
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
750 NC 0.4236079, 0.2408969 0.3322524
Ruletype
10203 T1wmorphology & T1wtexture & single-time-Enh & T2w
4971 T1wdynamic & T1wmorphology & T1wtexture & dispersion
12721 T1wdynamic & T1wmorphology & dispersion
1541 T1wmorphology & T1wtexture
715 T1wdynamic & T1wtexture & single-time-Enh
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
1338 T1wmorphology & T1wtexture
8424 T1wdynamic & T1wmorphology
6375 T1wmorphology & dispersion & T2w
750 T1wmorphology & T1wtexture
# print(FI[FI$allTestinfo.lesion_id==241,])
imgFI <- readPNG(paste0("Z:/Cristina/Section2/papernew_notes/images/", as.character(lesion_id),
"_", infoidx$cad_pt_no_txt, "_", infoidx$exam_a_number_txt, "_", infoidx$lesion_label, "_",
lesioninfo[lesioninfo$lesion_id == lesion_id, "find_t2_signal_int"], ".png"))
grid.raster(imgFI)
## with LMSIR
if (length(idLMSIR) > 0) {
for (i in 1:length(idLMSIR)) {
idx = idLMSIR[i]
lesion_id = FI[idx, ]$allTestinfo.lesion_id
print(lesion_id)
}
}
[1] 228
[1] 301
[1] 503
[1] 66
[1] 74
[1] 288
[1] 383
[1] 411
[1] 412
[1] 93
[1] 213
[1] 311
[1] 419
[1] 135
[1] 396
[1] 613
[1] 10
[1] 76
[1] 166
[1] 627
[1] 26
[1] 48
[1] 263
[1] 267
[1] 29
idx = c(1:nrow(FI))[c(FI$allTestinfo.lesion_id == lesion_id)]
infoidx = allTestinfo[allTestinfo$lesion_id == lesion_id, -c(20)]
print(infoidx)
lesion_id lesionfile cad_pt_no_txt anony_dob_datetime exam_img_dicom_txt
29 29 29_0168_5240535.vtk 0168 1958-03-27 00:00:00.000000 11164
exam_a_number_txt exam_dt_datetime exam_mri_cad_status_txt
29 5240535 2010-04-12 00:00:00.000000 Benign by pathology
cad_latest_mutation_status_int exam_find_mri_mass_yn exam_find_mri_nonmass_yn
29 Other 1 0
exam_find_side_int proc_pt_procedure_id proc_proc_dt_datetime proc_proc_side_int
29 Left 2798 2010-04-27 00:00:00.000000 Left
proc_proc_source_int proc_proc_guid_int proc_proc_tp_int
29 Radiology US Core Needle Biopsy
proc_lesion_comments_txt
29 CLINICAL INDICATION: Intraductal papillary lesion on recent\nbreast ultrasound 11 o'clock subareolar position left breast,\nrecommended for surgical excision biopsy. Recommended for MRI\nevaluation. Bilateral reduction mammoplasty 1990.
find_curve_int find_mri_dce_init_enh_int find_mri_dce_delay_enh_int BIRADS lesion_label
29 II Rapid Plateau 4 massB
lesion_diagnosis
29 FIBROCYSTIC
print(mypresentRules(eachFITopRules[[idx]], colnames(X), fnames))
len freq err
1233 4 0.066 0.028
1541 2 0.162 0.0570000000000001
12632 6 0.096 0.0580000000000001
1996 2 0.184 0.069
883 2 0.197 0.073
1338 2 0.193 0.077
7111 4 0.094 0.077
5547 5 0.17 0.087
3902 2 0.124 0.088
6375 4 0.202 0.092
750 2 0.25 0.094
condition
1233 enhancement-variance increasing rate(rim) low to medium & Max Margin Gradient low & Entropy ptime1 low & Sum average ptime2 very low to high
1541 irregularity low & Energy ptime4 low to medium
12632 Area Under Uptake curve(in) very low to high & Variance ptime1 very low & Energy ptime4 very low to high & dispersion s16 low to very high & 2nd post-SE s17 low to very high & 3rd post-SE s6 low to very high
1996 irregularity low & Energy ptime4 low to medium
883 irregularity low & Energy ptime4 low to medium
1338 irregularity low & Energy ptime4 low to medium
7111 Initial Uptake slope(in) low to medium & Curvature at Time-to-peak(in) low to very high & dispersion s10 low to very high & 2nd post-SE s11 high
5547 circularity high & Sum average ptime2 very low to high & dispersion s0 very low to high & dispersion s5 low to very high & T2w std SI low to very high
3902 circularity high & T2w radial gradient variance medium to high
6375 irregularity low & dispersion s5 low to very high & dispersion s10 low to very high & predicted LMSIR low to very high
750 irregularity low & Inverse difference moment ptime4 low to medium
pred prob sumtempProb
1233 NC 0.4810853, 0.2872408, 0.4052440, 0.3282516 0.3754554
1541 NC 0.4792871, 0.2735542 0.3764207
12632 NC 0.4755872, 0.5433402, 0.4788114, 0.4381729, 0.4557238, 0.5067061 0.4830569
1996 NC 0.5007048, 0.3009807 0.4008427
883 NC 0.4694149, 0.2405692 0.3549921
1338 NC 0.4991863, 0.2996197 0.399403
7111 NC 0.4452511, 0.5362599, 0.3412410, 0.4844197 0.4517929
5547 NC 0.3789780, 0.4486299, 0.4679563, 0.4074943, 0.4236785 0.4253474
3902 NC 0.5514954, 0.4847561 0.5181258
6375 NC 0.4029223, 0.4694528, 0.4305508, 0.4448463 0.4369431
750 NC 0.4236079, 0.2408969 0.3322524
Ruletype
1233 T1wdynamic & T1wmorphology & T1wtexture
1541 T1wmorphology & T1wtexture
12632 T1wdynamic & T1wtexture & dispersion & single-time-Enh
1996 T1wmorphology & T1wtexture
883 T1wmorphology & T1wtexture
1338 T1wmorphology & T1wtexture
7111 T1wdynamic & dispersion & single-time-Enh
5547 T1wmorphology & T1wtexture & dispersion & T2w
3902 T1wmorphology & T2w
6375 T1wmorphology & dispersion & T2w
750 T1wmorphology & T1wtexture
